Dipole-induced self-assembly of helical beta-peptides

In this work, the interactions between beta-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical beta-peptides using molecular dynamics simulations. The stability of a beta-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1-50 mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.     

Tuning secondary structure and self-assembly of amphiphilic peptides

Self-assembly is one of nature's mechanisms by which higher order structures are obtained. Two of the main driving forces for self-assembly, hydrophobic interactions and hydrogen bonding, are both present within amphiphilic peptides. Here, it is demonstrated how the intricately interconnected folding and assembly behavior of an N-terminally acylated peptide, with the sequence GANPNAAG, has been tuned by varying its hydrophobic tail and thermal history. The change in interplay between hydrophobic forces and peptide folding allowed the occurrence of different types of aggregation, from soluble peptides with a random coil conformation to aggregated peptides arranged in a beta-sheet assembly, which form helically twisted bilayer ribbons.     

Anion-directed self-assembly of coordination polymer into tunable secondary structure

A bent-shaped bipyridine ligand containing a dendritic aliphatic side chain has been synthesized as a ligand and complexed with silver ion through a self-assembling process. The resulting complexes were observed to self-assemble into supramolecular structures that differ significantly as a function of the counteranion size in the solid state, as confirmed by 1-D and 2-D X-ray diffraction experiments. The secondary structure of a cationic coordination chain appears to be dependent on the size of the counteranion. As the size of anion increases, the secondary structure of the coordination chain changes, from a helical chain, via a dimeric cycle, to a zigzag chain in the solid state. Interestingly, dilute solutions of the complexes exhibiting a columnar structure in polar solvents undergo spontaneous gelation and the resulting gels display a significant Cotton effect in the chromophore of the aromatic unit. These results represent a significant example that small variation in the anion size can provide a useful strategy to manipulate the secondary structure of linear chain and thereby solid-state supramolecular structure.     

Synthesis and 12-helical secondary structure of beta-peptides containing (2R,3R)-aminoproline

[structure: see text] (2R,3R)-Aminoproline, a pyrrolidine-based beta-amino acid, was synthesized and incorporated into hexa-beta-peptide 4. This residue confers water solubility when the ring nitrogen is protonated and allows for 12-helix formation in aqueous solution. Circular dichroism spectra display the 12-helical signature, and 12-helical structure was confirmed by 2D NMR analysis.     

Effect of secondary structure on the self-assembly of amphiphilic molecules: a multiscale simulation study

The self-assembly of amphiphilic molecules is of interest from a fundamental and practical standpoint. There has been recent interest in a class of molecules made from β-amino acids (which contain an additional backbone carbon atom when compared with natural amino acids). Block copolymers of β-peptides, where one block is hydrophobic and the other is hydrophilic, self-assemble into micelles. In this work, we use computer simulations to provide insight into the effect of secondary structure on the self-assembly of these molecules. Atomistic simulations for the free energy of association of a pair of molecules show that a homochiral hydrophobic block promotes self assembly compared to a heterochiral hydrophobic block, consistent with experiment. Simulations of a coarse-grained model show that these molecules spontaneously form spherical micelles.     

Effects of PEO length and phenyl unit structure on ionic conductivities of the complexes of LiClO4 and alternating copolymers of PEO having various phenyl units in the backbone

A series of copolymers of predominantly poly(ethylene oxide) (PEO) with mono-phenyl (HQ), biphenyl (BP) units, or both of them (HQ/BP) in the backbone were synthesized. The solid polymer electrolytes (SPEs) were prepared from three different types of copolymers (HQ-PEG, BP-PEG, and HQ/BP-PEG) employing lithium perchlorate (LiClO₄) as a lithium salt at a fixed salt concentration of [EO]/[Li⁺]=8. Their ionic conductivities were investigated to exploit the structure–ionic conductivity relationships as a function of structural change in rigid phenyl units and chain length ratio between flexible PEO chain and rigid phenyl units. As more rigid phenyl units were incorporated in the backbone chain, the formation inter- and intra-molecular complex with LiClO₄ became weaker and lower ionic conductivities were observed. And it was also found that higher ionic conductivity is obtained with increasing PEO chain length because inter- and intra-molecular dissociation power of PEO increases.     

Effects of template sequence and secondary structure on DNA-templated reactivity

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. As the size of DNA-templated libraries increases, the possibility of forming intramolecularly base-paired structures within templates that impede templated reactions increases as well. To achieve uniform reactivity across many template sequences and to computationally predict and remove any problematic sequences from DNA-templated libraries, we have systematically examined the effects of template sequence and secondary structure on DNA-templated reactivity. By testing a series of template sequences computationally designed to contain different degrees of internal secondary structure, we observed that high levels of predicted secondary structure involving the reagent binding site within a DNA template interfere with reagent hybridization and impair reactivity, as expected. Unexpectedly, we also discovered that templates containing virtually no predicted internal secondary structure also exhibit poor reaction efficiencies. Further studies revealed that a modest degree of internal secondary structure is required to maximize effective molarities between reactants, possibly by compacting intervening template nucleotides that separate the hybridized reactants. Therefore, ideal sequences for DNA-templated synthesis lie between two undesirable extremes of too much or too little internal secondary structure. The relationship between effective molarity and intervening nucleic acid secondary structure described in this work may also apply to nucleic acid sequences in living systems that separate interacting biological molecules.     

On the flexibility of beta-peptides

The full conformational space was explored for an achiral and two chiral beta-peptide models: namely For-beta-Ala-NH2, For-beta-Abu-NH2, and For-beta-Aib-NH2. Stability and conformational properties of all three model systems were computed at different levels of theory: RHF/3-21G, B3LYP/6-311++G(d,p)//RHF/3-21G, B3LYP/6-311++G(d,p), MP2//B3LYP/6-311++G(d,p), CCSD//B3LYP/6-311++G(d,p), and CCSD(T)//B3LYP/6-311++G(d,p). In addition, ab initio E = E(phi, micro, psi) potential energy hypersurfaces of all three models were determined, and their topologies were analyzed to determine the inherent flexibility properties of these beta-peptide models. Fewer points were found and assigned than expected on the basis of Multidimensional Conformational Analysis (MDCA). Furthermore, it has been demonstrated, that the four-dimensional surface, E = E(phi, mu, psi), can be reduced into a three-dimensional one: E = E[phi, f(phi), psi]. This reduction of dimensionality of freedom of motion suggests that beta-peptides are less flexible than one would have thought. This agrees with experimental data published on the conformational properties of peptides composed of beta-amino acid residues.     

Effects of conformational stability and geometry of guanidinium display on cell entry by beta-peptides

We have used our ability to control beta-peptide secondary structure in order to explore the effects of conformational stability and geometry of guanidinium display on cell entry. Both of these factors affect the rate and relative amount of beta-peptide accumulation in the cytoplasm and nucleus of live HeLa cells. These beta-peptides do not show significant differences in cell surface binding, implying that structure and guanidinium display are important in a later step in cell entry than initial surface binding.     

爪形大分子CTC-NO对柴油蜡晶结构和形态的影响

考察了爪形大分子CTC-NO(柠檬酸-1,4-丁二醇-柠檬酸-环烷酸-十八醇)对不同柴油的降滤效果,对蜡晶的形态进行了显微观察,利用XRD研究了蜡晶结构.结果表明:CTC-NO对不同柴油降滤效果不同,0#-3柴油降滤效果最好.加爪形大分子后蜡晶形态由规则片状转变为不规则的长形立体状、枝状、球状.XRD结果显示,加CTC-NO后晶粒尺寸变小、蜡晶结构改变.     

Effects of cationic and anionic nanoparticles on the stability of the secondary structure of DNA

The effects of anionic and cationic nanoparticles (15 and 100 nm in diameter) on the stability of the secondary structure of DNA were studied in DNA denaturation and renaturation processes. The results showed that DNA denaturation is greatly inhibited in the presence of cationic nanoparticles. In contrast, in the presence of even large amounts of anionic nanoparticles, the DNA melting transition occurs at the original melting temperature. The effects of the size and concentration of nanoparticles on DNA denaturation are discussed.     

Effects of DNA secondary structure on oligonucleotide probe binding efficiency

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable “window size” around target sites that is as small as possible without compromising folding algorithm prediction accuracy.     

Casein structure,self-assembly and gelation

The literature on recent studies of casein structure and function is reviewed. Where appropriate, we try to reconcile conflicting views on the issue of secondary structure in these proteins, steering a middle course where possible. A suggestion is put forward that a coarser view, treating the caseins as block copolymers may be sufficient to rationalise much of the behaviour of these proteins in self-association, adsorption and micellar assembly.     

11/9-mixed helices in the alpha/beta-peptides derived from alternating alpha- and beta-amino acids with proteinogenic side chains

alpha/beta-Hybrid peptides are prepared from amino acids with proteinogenic side chains on the basis of the concept of "alternating chirality", involving D-Phe and a beta3-hVal. Through the extensive NMR, CD, and MD studies, robust left-handed 11/9-mixed helices were identified in these peptides in CDCl3 solutions, wherein the 11/9-mixed helix was observed even in a small peptide with three residues.     

Theoretical study on tertiary structural elements of beta-peptides: nanotubes formed from parallel-sheet-derived assemblies of beta-peptides

Parallel or polar strands of beta-peptides spontaneously form nanotubes of different sizes in a vacuum as determined by ab initio calculations. Stability and conformational features of [CH3CO-(beta-Ala)k-NHCH3]l (1 < or = k < or = 4, 2 < or = l < or = 4) models were computed at different levels of theory (e.g., B3LYP/6-311++G(d,p)// B3LYP/6-31G(d), with consideration of BSSE). For the first time, calculations demonstrate that sheets of beta-peptides display nanotubular characteristics rather than two-dimensional extended beta-layers, as is the case of alpha-peptides. Of the configurations studied, k = l = 4 gave the most stable nanotubular structure, but larger assemblies are expected to produce even more stable nanotubes. As with other nanosystems such as cyclodextrane, these nanotubes can also incorporate small molecules, creating a diverse range of applications for these flexible, biocompatible, and highly stable molecules. The various side chains of beta-peptides can make these nanosystems rather versatile. Energetic and structural features of these tubular model systems are detailed in this paper. It is hoped that the results presented in this paper will stimulate experimental research in the field of nanostructure technology involving beta-peptides.