蛋白质与高分子的自组装

蛋白质是一类具有独特三维空间结构的生物高分子,其分子内部非共价键协同作用是形成三维空间结构的重要驱动力。同时,蛋白质分子与其他高分子之间也可以通过非共价键作用实现自组装。高分子链和蛋白质的结构特征是实现自组装的关键,溶液pH值、离子强度以及温度的变化会影响它们之间非共价键作用的类型和强度。本文归纳了水溶性高分子、嵌段共聚物和多糖与球状蛋白自组装的最新研究进展,分别从分子结构特征和溶液性质等因素讨论了其对高分子与蛋白质实现自组装的影响。其中,多糖与蛋白质的非共价键作用是化学与生物科学交叉领域最为活跃的研究课题之一,通过研究蛋白质与其他高分子的非共价键作用,对于理解和认识生命过程的本质与规律具有重要的意义,同时,在材料科学、纳米技术、食品科学等相关领域具有重要的应用价值。     

Energy minimizations with a combination of two knowledge-based potentials for protein folding

New force fields that are both simple and accurate are needed for computationally efficient molecular simulation studies to give insight into the actual features of the protein folding process. In this work, we assess a force field based on a new combination of two coarse-grained potentials taken from the bibliography. These potentials have already been proved efficient in representing different types of interactions, namely the side-chain interactions and the backbone hydrogen bonds. Now we combine them weighing their contribution to the global energy with a very simplified parameterization. To assess this combination of potentials, we use our evolutionary method to carry out energy minimization experiments for a set of all-alpha, all-beta, and (alpha + beta) protein structures. Our results, based on the assembly of short rigid native fragments, suggest that this combination of potentials can be successfully employed in coarse-grained folding simulations.     

Theory of main chain nematic polymers with spacers of varying degree of flexibility

Main chain liquid crystal polymers are modelled as either worms or jointed rods. In reality they are composed of mesogenic units (rods) linked by spacers with varying degrees of flexibility. We present a molecular model to describe non-homogeneous nematic polymers. The model takes account of molecular parameters, such as the lengths of the mesogenic group and the spacer units, and the interactions between them. The spacers are found to have an order differing from the mesogenic units. If the spacer is not very long and thus in effect is inflexible, one end of the spacer can retain to some extent the orientation of the other end, allowing orientational correlation between spacers mediated by the intermediate mesogenic unit. This is important in giving the chain a global rod-like behaviour as the nematic field becomes strong or the temperature low. The nematic order of the two components (mesogens and spacers), the nematic-isotropic transition as well as the latent entropy are examined. Furthermore, the anisotropic conformations of the polymers are investigated, which show either rod-like or random walk behaviour. Comparison of our results with experiment is found to be satisfactory.     

Solvent- and guest-responsive self-assembly of Hamilton receptor tethered bis(merocyanine) dyes

A novel supramolecular building block (8) that consists of a Hamilton receptor and two merocyanine dyes has been synthesized, and the self-assembly based on orthogonal hydrogen bonding and dipolar interactions has been studied in detail. Different self-assembled species, including oligomers, polymers, and inverted micelles could be observed upon variation of the solvent polarity and the concentration. Moreover, this system is highly responsive toward molecular stimuli such as merocyanine molecules with the barbituric acid motif that are bound by the Hamilton receptors. Detailed UV/Vis absorption studies provided insight into isodesmic or cooperative steps during the self-assembly of 8 into different species. The size of the aggregates in solution and the morphology on substrates have been explored by a combination of dynamic light scattering (DLS), atomic force microscopy (AFM), and TEM investigations.     

Towards mechanically-linked polymers

This short review describes the progress which is being made towards the self-assembly of mechanically-linked polymers. A new concept in polymer synthesis - self-assembly - is demonstrated to have the potential to create novel high molecular weight polymers which possess repeat units that do not just consist of a main chain backbone built up of entirely covalent bonds, but are constructed of mechanical linkages comprised of catenane and rotaxane motifs.     

Entropic barriers in nanoscale adhesion studied by variable temperature chemical force microscopy

Intermolecular interactions drive the vast majority of condensed phase phenomena from molecular recognition to protein folding to particle adhesion. Complex energy barriers encountered in these interactions include contributions from van der Waals forces, hydrogen bonding, and solvent medium. With the spectacular exception of hydrophobic interactions, contributions from the medium are usually considered secondary. We report a variable temperature force microscopy study of the interactions between several hydrogen bonds in different solvents that challenges this point of view. Surprisingly, we observed an increase in the strength of the interaction between carboxylic acid groups in ethanol as the temperature increased. Moreover, when we switched to a nonpolar solvent we observed the opposite behavior: The binding force decreased as the temperature increased. Kinetic model of bond dissociation provided quantitative interpretation of our measurements. We attributed the observed phenomena to a large entropic contribution from the ordered solvent layers that are forming on the probe and sample surfaces upon detachment. The observed reversal in the force vs temperature trend is a manifestation of a transition between thermodynamic and kinetic regimes of unbinding predicted by the model. Our results indicate that entropic barriers dominated by the interactions of solvent molecules with the surface exist in a much wider variety of systems than previously thought.     

Micellization,mixed micellization and solubilization: The role of interfacial interactions

The importance of interfacial Interactions in governing micellization, mixed micellization, polymer-micene complexation and solubilization is examined in this review. A common thermodynamic approach is used to treat these different phenomena involving surfactant self-assembly. In all the cases, the free energy of self-assembly can be decomposed into bulk and interfacial components. The interfacial component arises from two competing contributions. One is due to the free energy of formation of the micellar core-solvent interface while the other is due to the steric and electrostatic interactions among the head groups at the micellar surface. The competition between these two contributions is shown here as determining all the fundamental features of self-assembly. Specifically, we discuss in this review the influence of interfacial interactions on the cooperativity of self-assembly, the critical micelle concentration, the size and size distribution of micelles, the transition from spherical to cylindrical micelles, the non-ideal behavior in mixed surfactants, the complexation or non-complexation of micelles with polymers, the solubilization of aliphatic and aromatic hydrocarbons and the selective and synergistic solubilization of hydrocarbon mixtures.     

Using one‐step perturbation to predict the effect of changing force‐field parameters on the simulated folding equilibrium of a β‐peptide in solution

Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force‐field parameters. Here, we use the one‐step perturbation technique to predict the change of the free enthalpy of folding of a β‐peptide in methanol solution due to changing a variety of force‐field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut‐off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction‐field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom‐positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one‐step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one‐step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force‐field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

pH-Controlled Reversible Folding of Copolymers via Formation of β-sheet Secondary Structures

Protein functions are enabled by their perfectly arranged 3D structure, which is the result of a hierarchical intramolecular folding process. Sequence-defined polypeptide chains form locally ordered secondary structures (i.e., α-helix and β-sheet) through hydrogen bonding between the backbone amides, shaping the overall tertiary structure. To generate similarly complex macromolecular architectures based on synthetic materials, a plethora of strategies have been developed to induce and control the folding of synthetic polymers. However, the degree of complexity of the structure-driving ensemble of interactions demonstrated by natural polymers is unreached, as synthesizing long sequence-defined polymers with functional backbones remains a challenge. Herein, we report the synthesis of hybrid peptide-N,N-Dimethylacrylamide copolymers via radical Ring-Opening Polymerization (rROP) of peptide containing macrocycles. The resulting synthetic polymers contain sequence-defined regions of β-sheet encoding amino acid sequences. Exploiting the pH responsiveness of the embedded sequences, protonation or deprotonation in water induces self-assembly of the peptide strands at an intramacromolecular level, driving polymer chain folding via formation of β-sheet secondary structures. We demonstrate that the folding behavior is sequence dependent and reversible.     

Hydrogen-bonding-driven preorganized zinc porphyrin receptors for efficient complexation of C60, C70, and C60 derivatives

This paper describes the self-assembly of a new class of foldamer-based molecular tweezers, whose rigid folded conformations are stabilized by intramolecular hydrogen bonding. Two zinc porphyrin units are introduced to the ends of molecular tweezers Zn(2)1 and Zn(2)2, while three zinc porphyrin units are incorporated to the S-shaped bi-tweezers Zn(3)3, which may be regarded as a combination of two Zn(2)1 molecules. Due to the preorganized U-shaped feature, Zn(2)1 and Zn(2)2 are able to strongly complex C60, C70, and C60 derivative 25 in chloroform or toluene in a 1:1 binding stoichiometry, whereas Zn(3)3, which possesses two tweezer units, complexes the guests in a 1:2 stoichiometry. More stable complex Zn(3)3.24 is formed between Zn(3)3 and 24, a linear molecule bearing two C60 moieties at the ends, as a result of the cooperative interaction of two binding sites. Chiral induction is observed for all the three receptors upon complexation with C60-incoporated chiral phenylalanine derivative 29, although the complexation of 29 by the folding receptors is pronouncedly weaker than that of C60 and 25 due to increased steric hindrance. The driving force for the formation of the complexes is the well established pi-pi stacking between the zinc porphyrin and fullerene units. The 1H and 13C NMR, UV-vis, fluorescent, and circular dichroism spectroscopy have been used to investigate the complexing behavior of the folding receptors and the fullerene guests. The association constants of the corresponding complexes in toluene and chloroform (if possible) have been evaluated with the UV-vis and fluorescent titration experiments.     

Regulation of folding and photochromic reactivity of terarylenes through a host-guest interaction

The photochromic reactivity of terarylenes is integrated with molecular folding that is controlled through a host-guest interaction. A thieno[3,2,b]pyridine unit is introduced into a photochromic terarylene structure as an aryl unit to form a guest-interacting site. Thienopyridine-containing terarylenes showed solvent-dependent photochromic reactivity in solution. A terarylene moiety that contains two thienopyridyl units showed significantly high photocoloration reactivity as high as 88% of photocyclization quantum yield in methanol, whereas that value was only 24% in hexane. A temperature-dependent (1)H NMR spectroscopic study in different solvents indicated an interconversion between photochromic-reactive and unreactive conformations. In methanol, the intermolecular interaction between terarylene species and the solvent molecule slows the rate of interconversion and increases the population of the photochromic-active form, whereas the unreactive conformation is dominant in hexane. Crystal-structural studies demonstrated the perfect regulation of molecular folding between a photochromic-active form and an unreactive conformation by changing the solvents for recrystallization. Single crystals prepared from solutions in methanol showed reversible photochromic reactivity, whereas recrystallization from solutions in hexane did not show this reactivity. X-ray crystallographic studies of single crystals from solutions in methanol demonstrated that the photochromic molecules bind a solvent methanol molecule at the guest-interacting site to regulate the molecular conformation into a photochromic-active form in collaboration with specific intramolecular interactions, whereas crystals from solutions in hexane possess the photochromic-unreactive conformation.     

Synthesis of fullerodendrons with an ammonium unit at the focal point and their cooperative self-assembly on a fluorescent ditopic crown ether receptor

Dendritic branches with 1, 2, or 4 peripheral fullerene subunits and an ammonium function at the focal point have been prepared. Their ability to form self-assembled dendritic structures with oligophenylenevinylene receptors bearing one or two crown ether moieties has been evidenced by ES-MS studies for the first time. These supramolecular complexes are multicomponent photoactive devices in which the emission of the central receptor is dramatically quenched by the fullerene units. This new property resulting from the association of the different molecular subunits allowed detailed investigations of the self-assembly process by means of fluorescence titrations. The binding studies have revealed positive cooperative effects for the assembly of the fullerodendrimers with the ditopic receptor. Interestingly, the stability of the supramolecular 2:1 structures increases as the size of the dendritic unit increases. This positive dendritic effect has been explained by the larger number of possible intramolecular fullerene-fullerene interactions between the two dendritic guests when the number of fullerene subunits is increased.     

Liquid crystalline homopolyesters having main chain calamitic mesogens and one or two side chain azobenzene moieties in the repeat units

Combined semi-rigid homopolyesters, containing both main chain calamitic mesogens and one or two side chain azobenzene units separated by aliphatic (hexamethylene, octamethylene and decamethylene) chains in the polymer repeat units, were prepared and their liquid crystalline properties characterized. Polyesters having two side chain azobenzene units and a main chain biphenyl moiety showed a higher ordered smectic B or smectic F phase, whereas the other polymers containing a main chain 2,5-diphenyl-1,3,4-thiadiazole unit and one or two side chain methoxyazobenzene units formed a smectic C phase despite the presence of different mesogens in the main and side chains. This is probably due to the compact molecular chain-packing and intra- and intermolecular interactions between the polymer backbones and the two azobenzene units.     

Designer self-assembling peptide materials

Understanding of macromolecular materials at the molecular level is becoming increasingly important for a new generation of nanomaterials for nanobiotechnology and other disciplines, namely, the design, synthesis, and fabrication of nanodevices at the molecular scale from bottom up. Basic engineering principles for microfabrication can be learned through fully grasping the molecular self-assembly and programmed assembly phenomena. Self- and programmed-assembly phenomena are ubiquitous in nature. Two key elements in molecular macrobiological material productions are chemical complementarity and structural compatibility, both of which require weak and non-covalent interactions that bring building blocks together during self-assembly. Significant advances have been made during the 1990s at the interface of materials chemistry and biology. They include the design of helical ribbons, peptide nanofiber scaffolds for three-dimensional cell cultures and tissue engineering, peptide surfactants for solubilizing and stabilizing diverse types of membrane proteins and their complexes, and molecular ink peptides for arbitrary printing and coating surfaces as well as coiled-coil helical peptides for multi-length scale fractal structures. These designer self-assembling peptides have far reaching implications in a broad spectrum of applications in biology, medicine, nanobiotechnology, and nanobiomedical technology, some of which are beyond our current imaginations. [image: see text]     

Tandem catalysis and self-assembly: a one-pot approach to functionalized polymers

[reaction: see text] Side-chain functionalized polymers possessing terminal palladated SCS pincer complexes at each repeat unit were synthesized via ring-opening metathesis polymerization. These palladium centers function as both well-defined Heck catalysts and recognition units capable of quantitative self-assembly of pyridine-containing molecules. Exploitation of both the catalytic and self-assembly properties has led to the development of a controlled, one-pot tandem catalysis/self-assembly sequence for the synthesis of functionalized polymers.     

从超分子聚合物到超分子有机框架:组装溶液相超分子结构的周期性

单体分子在溶液相自发形成周期性的网络结构,是超分子化学和分子自组装研究领域的重大挑战.多头基分子在溶液相通过分子间非共价键作用可以形成超分子聚合物.提高多头基(三头基和四头基)分子骨架的刚性,可以提高结合位点的结构预组织,进而增强分子间相互作用的协同性和多价性特征,提高自组装结构的有序性或周期性.本文综述了多头基分子自组装形成超分子聚合物的一些重要进展,介绍了二维超分子有机框架(一类新的溶液相周期性自组装网络结构研究的最新进展.     

Developments in inorganic crystal engineering

The design and synthesis of crystalline materials through the self-assembly of molecular building blocks and the pursuit of functional materials based upon this approach are usually classified under the banner Crystal Engineering. The field is interdisciplinary in nature involving synthetic, materials, structural and theoretical chemists. There are strong ties to modern crystallography which can offer rapid and accurate structure determination and, in particular, insight into molecular and intermolecular geometries. Illustrative examples that chart the development field and provide an assessment of the current state of the art will be reviewed with an emphasis on inorganic chemistry. Broadly speaking, two classes of compounds will be discussed: those based upon molecules or ions linked into networks via noncovalent interactions and those (coordination polymers) in which metal centres are linked using coordination bonds through bridging ligands into extended networks.     

Biomolecules under mechanical stress: a simple mechanism of complex behavior

The unfolding of a biomolecule by stretching force is commonly treated theoretically as one-dimensional dynamics along the reaction coordinate coincident with the direction of pulling. Here we explore a situation, particularly relevant to complex biomolecules, when the pulling direction alone is not an adequate reaction coordinate for the unfolding or rupture process. We show that in this case the system can respond to pulling force in unusual ways. Our theory points out a remarkably simple, but largely overlooked, mechanism of the complex responses of biomolecules to force. The mechanism originates from the basic property of the transition state to change its structure under applied force. A relationship is established between a key experimental observable--force-dependent lifetime--and the microscopic properties of the biomolecule in the form of an analytical solution to the problem of a force-induced molecular transition in two dimensions. The theory is applicable to biological contexts ranging from protein folding to ligand-receptor interactions.     

Supramolecular polymers fabricated by orthogonal self-assembly based on multiple hydrogen bonding and macrocyclic host–guest interactions

Supramolecular polymers constructed by orthogonal self-assembly based on multiple hydrogen bonding and macrocyclic host-guest interactions have received increasing attention due to their elegant structures,outstanding properties,and potential applications.Hydrogen bonding endows these supramolecular polymers with good adaptability and reversibility,while macrocyclic host-guest interactions give them good selectivity and versatile stimuli-responsiveness.Therefore,functional supramolecular polymers fabricated by these two highly specific,noninterfering interactions in an orthogonal way have shown wide applications in the fields of molecular machines,electronics,soft materials,etc.In this review,we discuss the recent advances of functional supramolecular polymers fabricated by orthogonal self-assembly based on multiple hydroge n bonding and host-guest interactions.In particular,we focus on crown ether-and pillar[n]arene-based supramolecular polymers due to their compatibility with multiple hydrogen bonds in organic solution.The fabrication strategies,interesting properties,and potential applications of these advanced supramolecular materials are mainly concerned.