Amylose Dimerization in Solution Can Be Studied Using a Model System

Amylose, the linear polymer of α-1,4-linked glucopyranose units, is known to crystallize as a parallel double helix, but evidence of this duplex forming in solution has remained elusive for decades. We show how the dimerization of short amylose chains can be detected in solution using NMR spectroscopy when the glucans are labeled at the reducing-end with an aromatic moiety that overcomes chemical shift degeneracy leading to distinct signals for the single-stranded and duplex amylose. A set of α-1,4 glucans with varying lengths of 6, 12, 18, and 22 glucose units and a 4-aminobenzamide label were synthesized, enabling the first systematic thermodynamic study of the association of amylose in solution. The dimerization is enthalpically driven, entropically unfavorable and beyond a minimum length of 12, each additional pair of glucose residues stabilizes the duplex by 0.85 kJ mol-1 . This fundamental knowledge provides a basis for a quantitative understanding of starch structure, gelation and enzymatic digestion, and lays the foundations for the strategic use of α-1,4-glucans in the development of self-assembled materials.

Ligand-induced incompatible curvatures control ultrathin nanoplatelet polymorphism and chirality

The ability of thin materials to shape-shift is a common occurrence that leads to dynamic pattern formation and function in natural and man-made structures. However, harnessing this concept to rationally design inorganic structures at the nanoscale has remained far from reach due to a lack of fundamental understanding of the essential physical components. Here, we show that the interaction between organic ligands and the nanocrystal surface is responsible for the full range of chiral shapes seen in colloidal nanoplatelets. The adsorption of ligands results in incompatible curvatures on the top and bottom surfaces of the NPL, causing them to deform into helicoïds, helical ribbons, or tubes depending on the lateral dimensions and crystallographic orientation of the NPL. We demonstrate that nanoplatelets belong to the broad class of geometrically frustrated assemblies and exhibit one of their hallmark features: a transition between helicoïds and helical ribbons at a critical width. The effective curvature [Formula: see text] is the single aggregate parameter that encodes the details of the ligand/surface interaction, determining the nanoplatelets' geometry for a given width and crystallographic orientation. The conceptual framework described here will aid the rational design of dynamic, chiral nanostructures with high fundamental and practical relevance.

Hierarchical Serpentine-Helix Combination for 3D Stretchable Electronics

3D stretchable electronics attract growing interest due to their new and more complex functionalities compared to 1D or 2D counterparts. Among all 3D configuration designs, a 3D helical structure is commonly used as it can be designed to achieve outstanding stretching ratios as well as highly robust mechanical performance. However, the stretching ratio that mainly focuses on the axis direction hinders its applications. Inspired by hierarchies in a tendon, a novel structural design of hierarchical 3D serpentine-helix combination is proposed. The structural design constructed by a sequence with repeating small units winding in a helical manner around the axis can enable large mechanical forces transferred down to a smaller scale with the dissipation of potentially damaging stresses by microscale buckling, thereby endowing the electronic components made from high-performance but hard-to-stretch materials with large stretchability (≥200%) in x-, y-, or z-axis direction, high structural stability, and extraordinary electromechanical performance. Two applications including a wireless charging patch and an epidermal electronic system are demonstrated. The epidermal electronic system made of several hierarchical 3D serpentine-helix combinations allows for high-fidelity monitoring of electrophysiological signals, galvanic skin response, and finger-movement-induced electrical signals, which can achieve good tactile pattern recognition when combined with an artificial neural network.

Synthesis and Crystallographic Characterization of Helical Hairpin Oligourea Foldamers

Oligomers designed to form a helix-turn-helix super-secondary structure have been prepared by covalently bridging aliphatic oligourea foldamer helices with either rigid aromatic or more flexible aliphatic spacers. The relative helix orientation in these dimers has been investigated at high resolution using X-ray diffraction analysis. In several cases, racemic crystallography was used to facilitate crystallization and structure determination. All structures were solved by direct methods. Well-defined parallel helical hairpin motifs were observed in all cases when 4,4'-methylene diphenyl diisocyanate was employed as a dimerizing agent, irrespective of primary sequence and chain length.

Methods for characterizing the structure of starch in relation to its applications: a comprehensive review

Starch is a major part of the human diet and an important material for industrial utilization. The structure of starch granules is the subject of intensive research because it determines functionality, and hence suitability for specific applications. Starch granules are made up of a hierarchy of complex structural elements, from lamellae and amorphous regions to blocklets, growth rings and granules, which increase in scale from nanometers to microns. The complexity of these native structures changes with the processing of starch-rich ingredients into foods and other products. This review aims to provide a comprehensive review of analytical methods developed to characterize structure of starch granules, and their applications in analyzing the changes in starch structure as a result of processing, with particular consideration of the poorly understood short-range ordered structures in amorphous regions of granules.

Spacer-Dependent Cooperativity of Helicity in Fluorescent Bishelical Foldamers Based on L-Shaped Dibenzopyrrolo[1,2-a][1,8]naphthyridine

For the construction of helical foldamers composed of π-frameworks, the choice of appropriate π-π stacking units and π-spacers connecting them is important. The transfer of helicity between the minimal helix structural units is also an essential factor in the construction of homochiral helical foldamers. Tetramers 4 a-4 d, which have four L-shaped dibenzopyrrolo[1,2-a]naphthyridine units, were synthesized to investigate the interplay and cooperativity of the helical structures. Tetramer 4 a bridged with a biphenyl unit formed a homochiral bishelical structure with π-π stacking between the L-shaped units (3.3 Å), consisting only of (P,P)- and (M,M)-enantiomers without the (P,M)-diastereomer, owing to interplay through the axial chirality of biphenyl unit in the solid state. Similarly, in solution, thermodynamic stabilization of the two helix formations worked cooperatively to favor the bishelical form of 4 a. Furthermore, bishelical foldamer 4 a emitted intense fluorescence (Φ=0.86).

Macroscalar Helices Co-Assembled from Chirality-Transferring Temperature-Responsive Carbohydrate-Based Bolaamphiphiles and 1,4-Benzenediboronic Acid

We present the first example of macroscalar helices co‐assembled from temperature‐responsive carbohydrate‐based bolaamphiphiles (CHO‐Bolas) and 1,4‐benzenediboronic acid (BDBA). The CHO‐Bolas contained hydrophilic glucose or mannose moieties and a hydrophobic coumarin dimer. They showed temperature‐responsive reversible micelle‐to‐vesicle transition (MVT) in aqueous solutions. After the binding of carbohydrate moieties with boronic acids of BDBA in their alkaline solutions, right‐handed helices were formed via the temperature‐driven chirality transfer of d‐glucose or d‐mannose from the molecular to supramolecular level. These helices were co‐assembled by unreacted BDBA, boronate esters (B−O−C bonds) between CHO‐Bolas and BDBA, as well as boroxine anhydrides (B−O−B bonds) of self‐condensed BDBA. After heating at 300 °C under nitrogen, the helices displayed excellent morphological stability. Moreover, they emitted bright blue luminescence caused by strong self‐condensation of BDBA and decomposition of coumarin dimers.

Anion Transmembrane Nanochannels from Pore-Forming Helices Constructed by the Dynamic Covalent Reaction of Dihydrazide and Dialdehyde Units

Anion transmembrane nanochannels constructed from dynamic covalent helices (DCHs) are reported. The dynamic covalent structures can be synthesized by one-pot dynamic covalent reactions and helically self-fold into nanotubes through intramolecular hydrogen bonding and π-π interactions. Such helical structures can vertically self-assemble into long nanofibers under π-π stacking and their hollow nanocavities finally form ion permeation pathways across the lipid membranes. Single-channel electrophysiology signals provide solid evidence of DCHs following the channel rather than the carrier mechanism. Owing to the pore-forming capacity of DCHs, nanochannels are able to accelerate the movement of anions across lipid membranes with high transport activity (EC₅₀ =0.08 mol %). Moreover, DCH channels show dehydration energy dependent anion selectivity. This report highlights the importance of such DCHs as general channel scaffolds with economical synthesis and special nanocavities.

Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains

A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by ¹ H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.

Protein secondary structure motifs: A kinematic construction

The kinematic geometry of protein backbone structures, constrained by either single or multiple hydrogen bonds (H-bonds), possibly in a periodic array, is discussed. These structures include regular secondary structure elements α-helices and β-sheets but also include other short H-bond stabilized irregular structural elements like β-turns. The work here shows that the variations observed in such structures have simple geometrical correlations consistent with constrained motion kinematics. A new classification of the ideal helices is given, in terms of the parameter α, the angle at a C_α atom to its two neighboring C_α 's along the helix, and shown how it can be generalized to include nonideal helices. Specifically, we derive an analytical expression of the backbone dihedrals, (ϕ, ψ), in terms of the parameter α subject to the constraint that the peptide planes are parallel to the helical axis. Helices constructed in this way exhibit near-vertical alignment of the C = O and N - H units and are the canonical objects of this study. These expressions are easily modifiable to include perturbations of parameters relevant to nonplanar peptide units and noncanonical angles. The addition of a second parameter, ε₀ , inclination of successive peptide planes along a helix with respect to the helical axis leads to a generalization of the previous expression and provides an efficient parametrization of such structures in terms of coordinates consistent with H-bond parameters. An analogs parametrization of β-turns, using inverse kinematic methods, is also given. Besides offering a unifying viewpoint, our results may find useful applications to protein and peptide design.

Expanding 3D Nanoprinting Performance by Blurring the Electron Beam

Additive, direct-write manufacturing via a focused electron beam has evolved into a reliable 3D nanoprinting technology in recent years. Aside from low demands on substrate materials and surface morphologies, this technology allows the fabrication of freestanding, 3D architectures with feature sizes down to the sub-20 nm range. While indispensably needed for some concepts (e.g., 3D nano-plasmonics), the final applications can also be limited due to low mechanical rigidity, and thermal- or electric conductivities. To optimize these properties, without changing the overall 3D architecture, a controlled method for tuning individual branch diameters is desirable. Following this motivation, here, we introduce on-purpose beam blurring for controlled upward scaling and study the behavior at different inclination angles. The study reveals a massive boost in growth efficiencies up to a factor of five and the strong delay of unwanted proximal growth. In doing so, this work expands the design flexibility of this technology.

Oligo-Quinolylene-Vinylene Foldamers

Quinoline based aromatic amide foldamers are known to adopt stable folded conformations. We have developed a synthetic approach to produce similar oligomers where all amide bonds, or part of them, have been replaced by an isosteric vinylene group. The results of solution and solid state structural studies show that oligomers exclusively containing vinylene linkages are not well folded, and adopt predominantly flat conformations. In contrast, a vinylene segment flanked by helical oligoamides also folds in a helix, albeit with a slightly lower curvature. The presence of vinylene functions also result in an extension of π-conjugation across the oligomer that may change charge transport properties. Altogether, these results pave the way to foldamers in which both structural control and specific electronic properties may be engineered.

Aromatic Helical Foldamers as Nucleophilic Catalysts for the Regioselective Acetylation of Octyl β-d-Glucopyranoside

Two indolocarbazole-naphthyridine foldamers 2 and 3 that fold into helical conformations were prepared. The 4-(N,N-dimethylamino)pyridine (DMAP) moiety was introduced at one end of the foldamer strands to develop foldamer-based catalysts for the site-selective acylation of polyols. These foldamers adopt helical conformations containing internal cavities capable of binding octyl β-d-glucopyranoside. The association constants were determined to be 1.9 (±0.1)×10⁵  M^-1 for 2 and 2.1 (±0.1)×10⁵  M^-1 for 3 in CH₂ Cl₂ at 25 °C. In the presence of DMAP, 2 or 3 as the catalysts, octyl β-d-glucopyranoside was subjected to acetylation under identical reaction conditions. The DMAP-catalysed reaction afforded the random distribution of the monoacetylates (6-OAc : 4-OAc : 3-OAc : 2-OAc=33 : 24 : 41 : 2). In contrast, foldamers 2 and 3 led to the predominant formation of 6-OAc. The relative distributions were estimated to be 6-OAc : 4-OAc : 3-OAc=88 : 4 : 6 : ∼0 with 2 and 6-OAc : 4-OAc : 3-OAc : 2-OAc=90 : 3 : 6 : 1 with 3.

The Diverse World of Foldamers: Endless Possibilities of Self-Assembly

Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.

Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features

Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.

Advanced Actuator Materials Powered by Biomimetic Helical Fiber Topologies

Helical constructs are ubiquitous in nature at all size domains, from molecular to macroscopic. The helical topology confers unique mechanical functions that activate certain phenomena, such as twining vines and vital cellular functions like the folding and packing of DNA into chromosomes. The understanding of active mechanical processes in plants, certain musculature in animals, and some biochemical processes in cells provides insight into the versatility of the helix. Most of these natural systems consist of helically oriented filaments embedded in a compliant matrix. In some cases, the matrix can change volume and in others the filaments can contract and the matrix is passive. In both cases, the helically arranged fibers determine the overall shape change with a great variety of responses involving length contraction/elongation, twisting, bending, and coiling. Synthetic actuator materials and systems that employ helical topologies have been described recently and demonstrate many fascinating and complex shape changes. However, significant new opportunities exist to mimic some of the most remarkable actions in nature, including the Vorticella's coiling stalk and DNA's supercoils, in the quest for superior artificial muscles.

Halogen Bonding Helicates Encompassing Iodonium Cations

The first halonium-ion-based helices were designed and synthesized using oligo-aryl/pyridylene-ethynylene backbones that fold around reactive iodonium ions. Halogen bonding interactions stabilize the iodonium ions within the helices. Remarkably, the distance between two iodonium ions within a helix is shorter than the sum of their van der Waals radii. The helical conformations were characterized by X-ray crystallography in the solid state, by NMR spectroscopy in solution and corroborated by DFT calculations. The helical complexes possess potential synthetic utility, as demonstrated by their ability to induce iodocyclization of 4-penten-1-ol.

Wet-Chemical Synthesis of Chiral Colloids

We disclose a method for the synthesis of chiral colloids from spontaneously formed hollow sugar-surfactant microtubes with internally confined mobile colloidal spheres. Key feature of our approach is the grafting of colloid surfaces with photoresponsive coumarin moieties, which allow for UV-induced, covalent clicking of colloids into permanent chains, with morphologies set by the colloid-to-tube diameter ratio. Subsequent dissolution of tube confinement yields aqueous suspensions that comprise bulk quantities of a variety of linear chains, including single helical chains of polystyrene colloids. These colloidal equivalents of chiral (DNA) molecules are intended for microscopic study of chiral dynamics on a single-particle level.

Mesoscale Block Copolymers

Materials composed of well-defined mesoscale building blocks are ubiquitous in nature, with noted ability to assemble into hierarchical structures possessing exceptional physical and mechanical properties. Fabrication of similar synthetic mesoscale structures will offer opportunities for precise conformational tuning toward advantageous bulk properties, such as increased toughness or elastic modulus. This requires new materials designs to be discovered to impart such structural control. Here, the preparation of mesoscale polymers is achieved by solution fabrication of functional polymers containing photoinduced chemical triggers. Subsequent photopatterning affords mesoscale block copolymers composed of distinct segments of alternating chemical composition. When dispersed in appropriate solvents, selected segments form helices to generate architectures resembling block copolymers, but on an optically observable size scale. This approach provides a platform for producing mesoscale geometries with structural control and potential for driving materials assembly comparable to examples found in nature.

Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3₁₀-helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3₁₀ and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

C11 /C9 Helical Folding in αβ Hybrid Peptides Containing 1-Amino-cyclohexane acetic acid (β3, 3 -Ac6 c)

The present study describes the solid-state conformation of αβ hybrid peptides, Boc-Leu-β^3, 3 -Ac₆ c-OH, P1; Boc-Leu-β^3, 3 -Ac₆ c-Leu-β^3, 3 -Ac₆ c-OMe, P2; and Boc-Leu-β^3, 3 -Ac₆ c-Leu-β^3, 3 -Ac₆ c-Leu-OMe, P3. The dipeptide P1 adopts extended conformations, whereas tetrapeptide P2 and pentapeptide P3 favor a helical conformation stabilized by mixed types of C₁₁ /C₉ intramolecular hydrogen bonds. In peptide P3, the amino group of β^3, 3 -Ac₆ c(2) and β^3, 3 -Ac₆ c(4) residues occupies axial orientation, whereas in P2 it occupies axial and equatorial orientations for residues β^3, 3 -Ac₆ c(2) and β^3, 3 -Ac₆ c(4), respectively. The self-assembly of P3 forms channels filled with solvent molecules that present interesting patterns.

Reconfigurable Microscale Frameworks from Concatenated Helices with Controlled Chirality

The utility of helical structures in driving motion of microorganisms and plants has inspired efforts to develop synthetic stimuli-responsive helical architectures for self-motile and shape-morphing systems. While several approaches to responsive helices based on hydrogels and liquid crystalline polymers have been reported, they have so far been limited to macroscopic (cm scale) dimensions, and have not been applied to concatenated helices with more than two segments. Here, a robust method for microfabrication of helices inspired by Bauhinia seedpods, based on trilayer samples consisting of rigid plastic stripes sandwiching a swellable temperature-responsive hydrogel, is reported and the formation of responsive shape-controlled frameworks from concatenated multiple helices (multihelices) with controlled chirality is demonstrated. The block angle at each helical junction is controlled by the change in stripe direction, while the torsion angle defined by each segment of three helices is prescribed by the net twist of the middle segment, providing simple geometric design rules for the fabrication of complex 3D structures. This work opens new directions in programming 3D shapes by providing new insight into helical segments as building blocks, with potential applicability to the fabrication of scaffolds for cell culture, reconfigurable microfluidic channels, and microswimmers.

High-Power Actuation from Molecular Photoswitches in Enantiomerically Paired Soft Springs

Motion in plants often relies on dynamic helical systems as seen in coiling tendrils, spasmoneme springs, and the opening of chiral seedpods. Developing nanotechnology that would allow molecular-level phenomena to drive such movements in artificial systems remains a scientific challenge. Herein, we describe a soft device that uses nanoscale information to mimic seedpod opening. The system exploits a fundamental mechanism of stimuli-responsive deformation in plants, namely that inflexible elements with specific orientations are integrated into a stimuli-responsive matrix. The device is operated by isomerization of a light-responsive molecular switch that drives the twisting of strips of liquid-crystal elastomers. The strips twist in opposite directions and work against each other until the pod pops open from stress. This mechanism allows the photoisomerization of molecular switches to stimulate rapid shape changes at the macroscale and thus to maximize actuation power.

Simultaneous Adjustment of Size and Helical Sense of Chiral Nanospheres and Nanotubes Derived from an Axially Racemic Poly(phenylacetylene)

Nanospheres and nanotubes with full control of their size and helical sense are obtained in chloroform from the axially racemic chiral poly(phenylacetylene) poly-(R)-1 using either Ag⁺ as both chiral inducer and cross-linking agent or Na⁺ as chiral inducer and Ag⁺ as cross-linking agent. The size is tuned by the polymer/ion ratio while the helical sense is modulated by the polymer/cosolvent (i.e., MeCN) ratio. In this way, the helicity and the size of the nanoparticles can be easily interconverted by very simple experimental changes.

Hexagonal Lyotropic Liquid Crystal from Simple "Abiotic" Foldamers

The motivation of foldamer chemistry is to identify novel building blocks that have the potential to imitate natural species. Peptides and peptide mimetics can form stable helical conformations and further self-assemble into diverse aggregates in water, where it is difficult to isolate a single helix. In contrast, most "abiotic" foldamers may fold into helical structures in solution, but are difficult to assemble into tertiary ones. It remains a challenge to obtain "abiotic" species similar to peptides. In this paper, a novel foldamer scaffold, in which p-phenyleneethynylene units are linked by chiral carbon atoms, was designed and prepared. In very dilute solutions, these oligomers were random coils. The hexamer and octamers could form a hexagonal lyotropic liquid crystal (LC) in CH2Cl2 when the concentrations reached the critical values. The microscopic observations indicated that they could assemble into the nanofibers in the LC. Interestingly, after some LC phases were diluted at room temperature, the nanofibers could be preserved. The good stabilities of the assemblies are possibly attributed to a more compact backbone and more rigid side chains.

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies

Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. Here, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the amino acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. The helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.

Silicon-Copper Helical Arrays for New Generation Lithium Ion Batteries

The helical array (with 10 atom % Cu) exhibits 3130 mAh g(-1) with 83% columbic efficiency and retains 83% of its initial discharge capacity after 100th cycle. Homogeneously distributed interspaces between the helical arrays accommodate high volumetric changes upon cycling and copper atoms form a conductive network to buffer the mechanical stress generated in the electrode while minimizing electrochemical agglomeration of Si. Also, ion assistance is believed to enhance the density of the helices at the bottom thus increasing the adhesion.

Constraining cyclic peptides to mimic protein structure motifs

Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.

Bacterial cytoskeleton suprastructures and their physical origin

Bacterial cytoskeletal filamentous proteins, like their eukaryotic counterparts, are key regulators and central organizers of many cellular processes including morphogenesis, cell division, DNA segregation and movement. Such filaments often organize themselves into complex structures within the prokaryotic cell, driven by molecular crowding and cation association, to form bundles (ParM), rings, toroids and helical spirals (FtsZ) or interwoven sheets (MreB). The formation of complex structures is essential for bacterial cytoskeleton function. Here, we highlight the suprastructures of the prokaryotic cytoskeleton that have been observed by high resolution in vitro electron microscopy and set them in perspective with in vivo observations. We discuss the underlying physical principles that lead to complex structure formation.

Structure of sickled erythrocytes and of sickle-cell hemoglobin fibers

Deoxyhemoglobin from patients homozygous for sickle-cell anemia (deoxyhb S) aggregates into long straight fibers. These may extend through most of the length of the sickled cell, forming either square or hexagonally packed bundles with lattice constants of 170-180 A. Each fiber is a tube made up of six thin filaments, which are wound around the tubular surface with a helical pitch of about 3000 A. Each filament is a string of single hemoglobin molecules linked end to end at intervals of 62 A in dry and 64 A in wet fibers. Molecules in neighboring filaments are in longitudinal register so that they form flat hexagonal rings; these rings are stacked so that successive ones are rotated about the fiber axis by 7.3 degrees . The whole structure repeats after about eight rings. In this structure each molecule makes contact with four neighbors. The likely orientation of the molecules and points of contact between them are discussed. Similar filaments are also observed in normal deoxygenated erythrocytes, but in much lower concentration and aggregated into fibers of irregular diameter. No filaments appear in oxygenated sickle, or normal, adult cells, nor in oxygenated or deoxygenated fetal cells.

The reverse turn as a polypeptide conformation in globular proteins

The reverse turn, involving four consecutive amino acids, as a tertiary conformation in globular proteins is defined in terms of dihedral angles, the C(1) (alpha)...C(4) (alpha) distance and the O(1)...H-N(4) hydrogen bond distance. In seven proteins we find 125 examples of turns, comprising 33% of the amino acids in these proteins, as compared with 34% of the residues forming helices and only 17% forming beta-sheets. The amino-acid compositions of turns, helices, and beta-sheets are analyzed in some detail. We find Asn and Gly mainly in turns, Pro in turns (and at the beginning of helices), and Glu in helices. In these turns a statistical survey indicates that 19% of Asp residues are in the first position, 33% of Pro residues are in the second position, 24% of Asn residues are in the third position, and 26% of Trp residues are in the fourth position.