A conventional an 2DCOS infrared approach to the kinetics of protein misfolding

Cell viability depends on the correct folding of the proteins involved in metabolism. Proteins are synthesized on the endoplasmic reticulum and must follow a pathway to a correct, metastable, tridimensional structure. Changes in structure or in environmental conditions can drive an instability of the folding conditions and produce non-active aggregates that in principle are proteolysed by the cellular mechanisms. However, these aggregates can be even more stable than the native proteins, escaping the cellular control. They can be classified as amorphous, if there is not a well-organized structural pattern, or ordered if a repetitive pattern is produced. These ordered structures, known as fibrils, are involved in many diseases. Infrared spectroscopy is a method of choice to study its formation because it is not affected by turbidity or the formation of high molecular weight aggregates. Moreover, in both cases, two bands characteristic of intermolecular β-sheets allow the monitoring of the aggregate formation. In both cases, the appearance of these bands involves a non-reversible path in protein folding. It has been suggested that a difference in the ordered structures involves an increasing in band intensity. This change can be the origin in variations on the 2DCOS maps. The synchronous map gives an overall idea of the process involved. The asynchronous is more informative because reflects the kinetic changes produced. The outcome of both processes, amorphous or ordered is that 2DCOS can provide a further insight to the knowledge of the kinetic processes giving rise to aggregated structures. This outcome could consist on the order in which the different secondary structures are prone to form the aggregates.     

Structure factors of dispersible units of carbon black filler in rubbers

We report the structures of dispersible units, a most fundamental but minimal dispersible structural unit of a carbon black (CB) filler that is formed in two kinds of rubber (polyisoprene and styrene-butadiene random copolymer) matrices under a given processing condition. The results obtained from various small-angle scattering techniques showed that the CB aggregates, as observed after the sonification of a CB/toluene solution, were a spherical shape composed of approximately nine primary CB particles fused together. In the rubber matrices, the aggregates clustered into higher order structures defined in this work as the dispersible units, which are the fundamental structural elements (or the "lower cutoff structures") that build up a higher order mass-fractal structure. Furthermore, we found that the morphology of the dispersible units strongly depended on the rubber matrix, although the mass-fractal dimensions remained unchanged.     

Hydrophobic Actuation of a DNA Origami Bilayer Structure

Amphiphilic compounds have a strong tendency to form aggregates in aqueous solutions. It is shown that such aggregation can be utilized to fold cholesterol‐modified, single‐layered DNA origami structures into sandwich‐like bilayer structures, which hide the cholesterol modifications in their interior. The DNA bilayer structures unfold after addition of the surfactant Tween 80, and also in the presence of lipid bilayer membranes, with opening kinetics well described by stretched exponentials. It is also demonstrated that by combination with an appropriate lock and key mechanism, hydrophobic actuation of DNA sandwiches can be made conditional on the presence of an additional molecular input such as a specific DNA sequence.     

Identification of Regions in Apomyoglobin that Form Intermolecular Interactions in Amyloid Aggregates Using High-Performance Mass Spectrometry

The formation of amyloid aggregates in human organs and tissues causes the development of incurable diseases. However, experimental studies of the mechanism of amyloid formation by proteins and the structural characteristics of amyloids are complicated because of the heterogeneity and high molecular weight of the aggregates. We used limited proteolysis and mass spectrometry for the identification of regions in the apomyoglobin polypeptide chain, which give rise to intermolecular interactions in amyloid structures. Tandem mass spectroscopy enabled the identification of regions in the myoglobin polypeptide chain, which form the core of amyloid structures. It was shown that the main structural elements for the formation of the core of amyloid fibrils in myoglobin were regions from 60 through 90 and from 97 through 124 amino acid residues. These regions coincide well with those theoretically predicted. This approach yielded important data on the structure of protein molecules in aggregates and on conformational rearrangements of apomyoglobin upon amyloid formation.     

Video enhanced differential interference contrast microscopy: Characterizing colloidal materials

Video enhanced differential interference contrast microscopy (VEDICM) permits an immediate, rapid characterization of association colloid aggregates and other colloidal aggregates by direct visualization on a television screen. Particles with sizes down to 500 A, their dynamics, fusion and slow flocculation can be directly pictured, recorded and analyzed in real time, freezeframe, slow motion or time lapse. It is precisely in the distance regime, 500–10,000 A, joining micellar chemistry to the field of biological structures, that classical techniques do have most difficulty. In this domain surfactant aggregates-vesicles, liposomes, microemulsions, microtubules-can exhibit an astonishing dynamic structural diversity and distribution of structures. These are highly sensitive to pH, salt, temperature, and surfactant concentration in ways which are partially understood at a theoretical level, but not formerly easily accessible.In this paper, the VEDICM technique is described and its ability to follow the spontaneous growth and fusion of vesicles upon changes in chemical environment is presented.Session lecture, Ninth International Conference on Non-Aqueous Solutions, Pittsburgh, PA, August 1984.     

Hierarchy of Asymmetry in Chiral Supramolecular Polymers: Toward Functional,Helical Supramolecular Structures

The formation of helical structures through the supramolecular polymerization of a variety of self-assembling units is reviewed. These scaffolds are usually obtained by efficient transfer or amplification of chirality phenomena, in which the starting self-assembling molecules possess different elements of asymmetry, such as point or axial chirality. Relevant examples of helical supramolecular structures investigated under thermodynamic control are reviewed, and the helical outcome of remarkable examples of chiral entities obtained through kinetic control are also highlighted. Finally, selected examples of flexible macroscopic chirality and catalysis are described to illustrate the applicability of helical aggregates.     

Introduction of curvature in amphipathic oligothiophenes for defined aggregate formation

In this study the possibility to control the size and shape of self-assembled structures through the local curvature of their molecular building blocks has been investigated. To this end a series of amphipathic conjugated oligothiophenes with a well-defined curvature of their backbone has been designed and synthesized. The molecular (local) curvature of these oligothiophenes resulted from a preference for cis instead of trans conformations at specific positions along the oligothiophene backbone, which can be controlled by the sequence of hydrophilic and hydrophobic groups, while their ratio was kept constant. The self-assembly of ter-, sexi-, and dodecathiophenes appeared to be a low-cooperative process, involving the formation of premicellar aggregates at sub-millimolar concentrations, which at concentrations in the millimolar regime transformed into micelles and cylindrical micelles. The aggregates display fine structures with dimensions reminiscent of the thiophene molecules. The structure-morphology relationship of the ter- and sexithiophenes could be described by conventional packing theory. However, with the dodecathiophene, the backbone curvature governed the formation of cylindrical aggregates with a well-defined diameter. These results demonstrate that it is possible to control the aggregation morphology of simple amphipathic oligothiophenes by implementation of an additional structural motif namely, the curvature.     

Formation of wormlike aggregates of fluorocarbon-hydrocarbon hybrid surfactant by Langmuir-Blodgett transfer and alignment of gold nanoparticles

A novel anionic fluorocarbon-hydrocarbon hybrid surfactant (SS-Hyb-Na+) with a disulfide group has been synthesized from 11-bromo-1-undecanal and perfluorohexylethyl iodide via three steps. The Langmuir-Blodgett (LB) transfer of the 1:100 (mol/mol) mixed monolayer of SS-Hyb-Na+ and stearyl alcohol (C18OH) formed on an aqueous solution containing a cationic polymer, poly(diallyldimethylammonium chloride) (PDDA+Cl-) onto a hydrophobic silicon wafer yields the formation of wormlike aggregates consisting of SS-Hyb-/PDDA+ polyion complexes. It is found that the aggregates align along the withdrawal direction of the wafer substrate. When the wafer on which the wormlike aggregates exist is immersed into the dispersion of gold nanoparticles (Au NPs) prepared by the citrate reduction method, Au NPs align along the wormlike structures. Even though the surface of the wafer is placed either vertical or parallel to the monolayer compression direction during the LB transfer, the one-dimensional (1D) array of Au NPs is observed along the withdrawal direction of the wafer. This indicates that the wormlike aggregates of SS-Hyb-/PDDA+ complexes are aligned during the LB transfer, and the aligned aggregates behave as a scaffold in the 1D array of Au NPs.     

Structural properties of nonionic cyclodextrin colloids in water

The amphiphilic character in water of a novel class of chemically modified cyclodextrins has been investigated by means of small-angle X-ray scattering and light scattering. The introduction ofhydrophilic oligo(ethylene glycol) onto the secondary side of heptakis[6-alkylthio-6-deoxy-2-oligo(ethylene glycol)]-beta-cyclodextrins produces an enhanced water solubility of these molecules. Shape and dimensions of the generated micellar aggregates, analyzed in terms of a suitable core-shell model, remain stable in the wide concentration range explored. The highly associative behavior of these macromolecules is evidenced by the very low value of the critical micelle concentration (cmc), which is about 2 orders of magnitude smaller than the cmc usually obtained for traditional surfactant. Despite the complex geometry of this novel macromolecule, shape and dimensions of generated micellar aggregates can be properly described according to the thermodynamic approaches generally used for amphiphilic molecules and block copolymers. Results show how the modulation of hydrophobic and hydrophilic components sensitively influence the structural features of the generated aggregates thus offering the possibility to control molecular organization in a manner similar to that for traditional colloids. For all the classes of the investigated systems, the small micelles have been found in equilibrium with polydisperse large aggregates of entangled micelles. These novel nonionic colloidal systems combine inclusion and transport properties of host macrocycles, such as cyclodextrin, together with the increased stability of colloidal aggregates, and may be of interest for their potential application as innovative drug delivery systems.     

Tubular hydrogen-bonded networks sustained by water molecules.

The design concept of functional solids relies on controlling the topology of crystal packing through exploitation of weak intermolecular forces. In the context of cyclic aggregates, the ability to anticipate the consequences of ring constituents and their stereochemistries on ring conformation is vitally important since even an apparently slight structural change effected on molecules can dramatically alter the crystal structure. We have found that solid-state structures formed by hydroxy acids with a general structure (+/-)-1 depend on steric interactions. Thus, with the exception of molecules 1b and 1e, compounds (+/-)-1a-(+/-)-1m, which possess bulky and conformationally rigid substituents, aggregate by forming tapes and sheets by alternating (+) and (-) subunits held together through carboxylic acid-to-alcohol hydrogen bonds. Homologue (+/-)-1n, with conformationally flexible substituents which allow conformational deformation, gives, by incorporation of molecules of water, an efficient hexagonal assembly which extends to the third dimension to form tubular H-bonding networks. Each puckered channel can be described as interconnected closely packed hexagons in chairlike conformations. The ethyl groups presented in (+/-)-1n gave the volume required to lock the inner hexagonal wall into a rigid structure. Attempts to obtain cyclic aggregates using small substituents, compounds (+/-)-1o-(+/-)-1q, failed. The observed supramolecular assemblies of the anhydrous compounds can be classified into one-dimensional strands and two-dimensional sheets, while three-dimensional networks are present only in the hydrated molecules (1b, 1e, and 1n). The crystal structure of the anhydrous (+/-)-1n compound confirms the important role played by water molecules in the formation of tubular structures.     

The degree of structural protection at the edge beta-strands determines the pathway of amyloid formation in globular proteins

The assembly of proteins into highly organized fibrillar aggregates is a key process in biology, biotechnology, and human disease. It has been shown that proteins retain a small, yet significant propensity to aggregate when they are folded into compact globular structures, and this may be physiologically relevant, particularly when considering that proteins spend most of their lifespan into such compact states. Proteins from the acylphosphatase-like structural family have been shown to aggregate via different mechanisms, with some members forming native-like aggregates as a first step of their aggregation process and others requiring unfolding as a first necessary step. Here we use the acylphosphatase from Sulfolobus solfataricus to show that assembly of folded protein molecules into native-like aggregates is prevented by single-point mutations that introduce structural protections within one of the most flexible region of the protein, the peripheral edge beta-strand 4. The resulting mutants do not form native-like aggregates, but can still form thioflavin T-binding and beta-structured oligomers, albeit more slowly than the wild-type protein. The kinetic data show that formation of the latter species proceeds via an alternative mechanism that is independent of the transient formation of native-like aggregates.     

Structure of hard-sphere fluid and precursor structures to crystallization

The structural origin of the commonly observed split second peak of the radial distribution function of a supercooled or glassy liquid is examined in this work using the hard-sphere fluid as an example. A novel approach to the analysis of the microscopic structure of a fluid is described, which permits the decomposition of both the radial distribution function and bond-angle distribution function of a system of particles into contributions from a small number of ring structures. The method uses a modified shortest-path definition of rings appropriate to the analysis of the medium-range structure of dense systems. It is shown that the split peak is an indicator of the emergence of precursor structures to crystal formation. The origin of the split peak provides a structural link between fluid and crystalline phases and our results suggest that it is neither a structural feature peculiar to glassy phases nor a smooth structural continuation of the stable-fluid phase. This structural feature of simple glassy systems is more appropriately described as a signifier of the frustration of emerging crystalline order in a fluid.     

Novel preparation of snowflake-like dendritic nanostructures of Ag or Au at room temperature via a wet-chemical route

In this letter we describe a novel but effective wet-chemical route for the simple preparation of snowflake-like dendritic nanostructures of Ag, which are homogeneous in size, carried out by directly mixing AgNO3 and p-phenylenediamine (PPD) aqueous solutions at room temperature. It reveals that such dendrites are aggregates of nanoparticles and highly crystalline in nature. It is found that the molar ratio of [PPD]/[Ag+] influences the final morphologies of the structures formed and that excessive PPD (the molar ratio of [PPD]/[Ag+] is higher than 1:1) is crucial to achieving dendrites. The possible dendritic growth mechanism is also predicted. This method can also be extended to the preparation of Au dendrites.     

6-氮杂吲唑类Pim-1激酶抑制剂的3D-QSAR、药效团模型研究和分子设计

Pim-1 激酶通过作用于多种信号通路或靶点影响肿瘤的发生发展,近年来被认为是肿瘤治疗的良好靶标。本文采用SYBYL-X2. 1. 1软件中的TopomerCoMFA、GALAHAD模块建立计算机模型,研究39个基于6-氮杂吲唑环的Pim-1激酶抑制剂的三维定量构效关系及药效团特征元素。结果显示,TopomerCoMFA建模所得交叉验证系数（q2）和相关系数（r2）分别为0. 756和0. 951,结合外部验证表明此3D-QSAR模型具有较高预测能力及较好的统计学稳定性,同时,用等势图描述了R1、R2基团处立体场、静电场对活性的具体影响。药效团研究结果表明,含氢键受体的芳香杂环母核结构,以及侧链取代基中含有芳香杂环结构对化合物的活性贡献较大。最后根据上述模型信息新设计了15个Pim-1激酶抑制剂分子并完成活性预测及分子对接模式研究,其中4个分子的预测pIC50高于建模分子中活性最好的化合物17,Surflex-Dock分析显示新设计分子均与Pim-1激酶形成较强氢键相互作用。基于6-氮杂吲唑环的Pim-1激酶抑制剂的3D-QSAR模型以及药效团模型可用于指导新型抑制剂的结构优化,为设计和开发具有较高活性的新型Pim-1激酶抑制剂提供有效帮助。     

Computer generation of chemical structures from known fragments

The interactive generation of chemical structures from given fragments is described and discussed. It is implemented as a part of our expert system CARBON, based on C-13 NMR spectra. As it is designed, this program can also be a useful tool in the structure elucidation process when information on parts of the structure is obtained by other means (IR, mass and other spectrometries, chemical analysis, other relevant information). The topological characteristics of candidate fragments are first chosen interactively and then the elements are connected in all topologically possible ways. In the following step, the topological building blocks are substituted by chemical structural fragments resulting in a set of all chemical structures consistent with the input information.     

共聚物的自组装研究进展

自组装是分子间通过非共价键相互作用自发组合形成的一类结构明确、稳定,同时具有某种特定功能或性能的分子聚集体或超分子结构的现象。利用共聚物自组装技术可以制备高度有序介观形貌的功能材料,这些材料有望在生物医学、药物释放、智能材料等领域得到广泛的应用。研究表明,不同结构的共聚物的自组装行为和功能一般不同,同时环境条件,如温度、pH值等也对共聚物自组装行为有很大影响。本文从共聚物结构及外部环境条件两个方面综述了近几年来共聚物的自组装行为规律,并分析了相关自组装结构应用的研究进展。     

Molecular theory of surfactant micelles in aqueous solution

This paper presents an overview of recent theoretical work on the molecular theory of micelle formation. A primary emphasis is given to the role of computer simulation of condensed materials in understanding micelle structure and thermodynamics. Much of the detailed discussion focuses on recent Monte Carlo studies of a simple molecular model of micellar aggregates. For clarity of presentation, a compact, physical organization of micelle thermodynamic equilibrium ratios is advocated. This procedure provides a simple basis for physical reasoning about the molecular roles of attractive and repulsive forces in micellization thermodynamics. The molecularly coarse-grained micellar structural information available from current small angle neutron scattering (SANS) measurements is surveyed. The structural predictions of the reviewed Monte Carlo calculations are shown to be in good qualitative agreement with the SANS data. The Monte Carlo results indicate that micelles should be viewed as fluid aggregates with a low surface free energy relative to water-hydrocarbon interfaces. The computer experimental results suggest that dynamic surface and shape fluctuations should be considered in understanding micelle structure at a molecular level. Several instantaneous structures are graphically displayed to illustrate that these transitory structures could be qualitatively described as “dry” but irregularly shaped. Configurations drawn from Monte Carlo calculations on cylindrical and bilayer structures of infinite extent are used to illustrate the role of surface flexibility in these systems.     

SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands

Summary SPLICE is a program that processes partial query solutions retrieved from 3D, structural databases to generate novel, aggregate ligands. It is designed to interface with the database searching program FOUNDATION, which retrieves fragments containing any combination of a user-specified minimum number of matching query elements. SPLICE eliminates aspects of structures that are physically incapable of binding within the active site. Then, a systematic rule-based procedure is performed upon the remaining fragments to ensure receptor complementarity. All modifications are automated and remain transparent to the user. Ligands are then assembled by linking components into composite structures through overlapping bonds. As a control experiment, FOUNDATION and SPLICE were used to reconstruct a know HIV-1 protease inhibitor after it had been fragmented, reoriented, and added to a sham database of fifty different small molecules. To illustrate the capabilities of this program, a 3D search query containing the pharmacophoric elements of an aspartic proteinase-inhibitor crystal complex was searched using FOUNDATION against a subset of the Cambridge Structural Database. One hundred thirty-one compounds were retrieved, each containing any combination of at least four query elements. Compounds were automatically screened and edited for receptor complementarity. Numerous combinations of fragments were discovered that could be linked to form novel structures, containing a greater number of pharmacophoric elements than any single retrieved fragment.     

Selecting folded proteins from a library of secondary structural elements

A protein evolution strategy is described by which double-stranded DNA fragments encoding defined Escherichia coli protein secondary structural elements (alpha-helices, beta-strands, and loops) are assembled semirandomly into sequences comprised of as many as 800 amino acid residues. A library of novel polypeptides generated from this system was inserted into an enhanced green fluorescent protein (EGFP) fusion vector. Library members were screened by fluorescence activated cell sorting (FACS) to identify those polypeptides that fold into soluble, stable structures in vivo that comprised a subset of shorter sequences ( approximately 60 to 100 residues) from the semirandom sequence library. Approximately 108 clones were screened by FACS, a set of 1149 high fluorescence colonies were characterized by dPCR, and four soluble clones with varying amounts of secondary structure were identified. One of these is highly homologous to a domain of aspartate racemase from a marine bacterium (Polaromonas sp.) but is not homologous to any E. coli protein sequence. Several other selected polypeptides have no global sequence homology to any known protein but show significant alpha-helical content, limited dispersion in 1D nuclear magnetic resonance spectra, pH sensitive ANS binding and reversible folding into soluble structures. These results demonstrate that this strategy can generate novel polypeptide sequences containing secondary structure.     

Supramolecular assemblies of quaternary ammonium cations and halide anions in the gas phase: ESMS-FTICR data and computer modelling

Supramolecular aggregates of tetraalkylammonium halides (R4NX) are formed by electrospray out of acetonitrile solution. Mass spectrometry reveals 88 charged aggregates for R= Me, Et, Bu; X= Br, I, ranging up to [(Bu4N)39Br42]3- in size. With the objective of improving calculations of intermolecular energies for supramolecular aggregates of ions, calibrated semi-empirical potentials for inter-ion interactions have been developed and applied to these aggregates. The accuracy of the calculated energies is supported by the measured collisional dissociation energy of (Et4N+)4 (I-)5. Energy optimisations indicate that the probable structures have the halide ions dispersed in a matrix of cations, which, for Bu4N+, can be mutually attractive. The aggregates are structurally fluid, with multiple structures separated by 4-8 kJmol(-1). The energy calculations are entirely consistent with the observed formation of large aggregates, and of multiply charged anions. It is estimated that the cohesive energies of supramolecular assemblies of ions such as these reach about 40 kJmol(-1) per constituent ion.