Comparative conformational analysis of peptide libraries

Six computer-based combinatorial libraries,including tetrapeptide sequences (generated with fiveamino acids) and conformations (generated with fivemain chain and three side chain rotamers), wereobtained and sequence-conformation probabilities werecalculated with a molecular and statistical mechanicsprocedure. The structural motifs -helix,-sheet, 3₁₀-helix, reverse turn I and-turn were focused in these calculations. Itis shown that sequence-conformation-probabilitysurfaces provide a broad view of structural changesaccompanying changes in sequence. Numerical indicesare defined to enable comparisons between frequenciesof occurrence of these structural motifs in peptidelibraries and in a database of low sequence identityprotein structures. Fine details ofsequence-conformation-probability surfaces show theeffect of point mutations. Broad comparisons betweendifferent regions of these surfaces indicate how toselect the occurrence of structural motifs in thecombinatorial synthesis of peptide chains.     

Exploring the chemical space of peptides for drug discovery: a focus on linear and cyclic penta-peptides

Peptide and peptide-like structures are regaining attention in drug discovery. Previous studies suggest that bioactive peptides have diverse structures and may have physicochemical properties attractive to become hit and lead compounds. However, chemoinformatic studies that characterize such diversity are limited. Herein, we report the physicochemical property profile and chemical space of four synthetic linear and cyclic combinatorial peptide libraries. As a case study, the analysis was focused on penta-peptides. The chemical space of the peptide and N-methylated peptides libraries was compared to compound data sets of pharmaceutical relevance. Results indicated that there is a major overlap in the chemical space of N-methylated cyclic peptides with inhibitors of protein–protein interactions and macrocyclic natural products available for screening. Also, there is an overlap between the chemical space of the synthetic peptides with peptides approved for clinical use (or in clinical trials), and to other approved drugs that are outside the traditional chemical space. Results further support that synthetic penta-peptides are suitable compounds to be used in drug discovery projects.     

Application of computer assisted combinatorial chemistry in antivirial,antimalarial and anticancer agents design

Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of Compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anti-cancer drugs. These illustrate library focusing strategies.     

Combinatorial chemistry of β-hairpins

Combinatorial chemistry is expanding rapidly both in terms of chemistry development and application to the synthesis of compound libraries for lead discovery and optimization. Combinatorial technologies continue evolving and developing, in fact they are being used as basic research tools in different fields that include peptide/protein folding. This review examines the use of combinatorial chemistry in the design of peptides and protein domains that adopt beta-sheet conformations. In particular, the use of conformationally restricted peptide libraries has allowed the identification of linear peptides that are folded in a beta-hairpin structure in plain aqueous solutions.     

Exploring antibody polyspecificity using synthetic combinatorial libraries

Summary Extensive mapping studies for seven antigen-antibody interactions have been carried out using both individual analogs and peptide libraries. With competitive ELISA, these studies have revealed that monoclonal antibodies exhibit a broad range of specificities, from antibodies that recognize only conservative substitutions for 1–2 positions of the antigenic determinant, to antibodies that recognize sequences that are completely unrelated to the parent antigen with comparable affinities. Synthetic combinatorial libraries, containing millions of peptide sequences, permit a more systematic and rapid evaluation of the extent of multiple-binding specificities of monoclonal antibodies than individual analogs. The peptide libraries used here comprise mixtures of compounds having specifically defined positions and mixture positions. The same diversity of sequences in different formats, which differ by the numbers of positions singularly defined and different locations defined within the sequence, can be examined. Comparison of the screening results, selection criteria of the most active mixtures, and different approaches used for the deconvolution of active individual compounds are discussed. Synthetic combinatorial libraries greatly facilitate the understanding of antigen-antibody interactions at the amino acid level and will assist in the development of improved immunodiagnostics.     

Utilization of multiple phage display libraries for the identification of dissimilar peptide motifs that bind to a B7-1 monoclonal antibody

Summary Seven random peptide libraries (two displaying linear peptides and five displaying cysteine-constrained peptides) were constructed as gene III fusion proteins of the bacteriophage fd-tet. These libraries were used to screen a blocking monoclonal antibody raised against B7-1 (CD80), a human cell surface antigen that binds two T cell receptors, CD28 and CTLA-4. After three rounds of screening against the immobilized antibody, 1000-fold enrichment was observed in libraries displaying both linear and cysteineconstrained peptides. DNA sequencing of the enriched phage revealed two distinct consensus sequences: HXG(A/Y)XH and DVCXXGGPGC. Phage expressing these consensus sequences bound to L307.4 but not to an isotype matched antibody, indicating that binding was antibody specific. Synthetic peptides corresponding to both motifs inhibited phage binding to L307.4, indicating that the gene III protein is not required for peptide binding. In addition, the cyclized forms of synthetic peptides containing the DVCXXGGPGC motif were capable of inhibiting L307.4 binding to soluble B7-1/Fc fusion. Moreover, phage expressing only the HXG(A/Y)XH consensus sequence were inhibited from binding to L307.4 by the presence of chelating agents. These results indicate that the framework within which the peptide is presented on the surface of the phage may allow the identification of unique peptide motifs with distinct binding characteristics. These peptide motifs could be used for the design of peptidomimetics with therapeutic applications if they inhibit the binding of B7-1 to its T cell receptors.     

A combinatorial method for constructing libraries of long peptides displayed by filamentous phage

Summary We describe the construction and screening of a random peptide library displayed by filamentous phage. The peptides are expressed in multiple copies on the filamentous phage M13 as amino-terminal fusions with the major coat protein, the product of gene VIII. These libraries are efficiently screened for reactive peptides, using a combination of panning in solution followed by a plaque lift assay. Advantages of this system are that both high- and low-affinity phage clones are simultaneously identified and the analysis of non-reactive phage is minimized. The vector system utilized to construct this library enables it to be used for the construction of peptide libraries employing a combinatorial cloning strategy. This feature makes it especially suitable for construction of peptide libraries using codon-based oligonucleotide synthesis. The vectors also allow rapid optimization and modification of lead peptides by codon-based mutagenesis. A 20-amino acid long random peptide library of 1 × 10⁹ members was constructed and screened for peptides that bound to (i) a monoclonal antibody recognizing the amino-terminus of -endorphin; (ii) a monoclonal antibody recognizing a peptide epitope derived from the v -ros oncogene product; and (iii) the constant region of murine IgG2b. The approach described here provides a means for the construction of customized libraries that can be screened with a variety of target molecules.     

Structure and properties of TentaGel resin beads: Implications for combinatorial library chemistry

Summary In view of the widespread use of TentaGel resin beads for the synthesis of combinatorial libraries, the properties of TentaGel resin have been examined using a combination of confocal laser microscopy and NMR spectroscopy. Evidence is presented that trypsin, a 23.5-kDa enzyme, can penetrate to the core of 90-m TentaGel beads, and that the matrix of such beads permits molecular motion at a similar rate to that in solution. The beads act as a separate gel phase rather than as a porous solid. These conclusions have important implications for the bioassay of on-bead combinatorial chemical libraries.     

Microstructure and structural phase transitions in iron-based superconductors

Crystal structures and microstructural features, such as structural phase transitions, defect structures, and chemical and structural inhomogeneities, are known to have profound effects on the physical properties of superconducting materials. Recently, many studies on the structural properties of Fe-based high-Tc superconductors have been published. This review article will mainly focus on the typical microstructural features in samples that have been well characterized by physical measurements. （i） Certain common structural features are discussed, in particular, the crystal structural features for different superconducting families, the local structural distortions in the Fe2Pn2 （Pn = P, As, Sb） or FeeCh2 （Ch = S, Se, Te） blocks, and the structural transformations in the 122 system. （ii） In FeTe（Se） （11 family）, the superconductivity, chemical and structural inhomogeneities are investigated and discussed in correlation with superconductivity. （iii） In the Ko.sFe1.6＋xSe2 system, we focus on the typical compounds with emphasis on the Fe-vacancy order and phase separations. The microstructural features in other superconducting materials are also briefly discussed.     

Molecular diversification in spider venoms: A web of combinatorial peptide libraries

Summary Spider venoms are a rich source of novel pharmacologically and agrochemically interesting compounds that have received increased attention from pharmacologists and biochemists in recent years. The application of technologies derived from genomics and proteomics have led to the discovery of the enormous molecular diversity of those venoms, which consist mainly of peptides and proteins. The molecular diversity of spider peptides has been revealed by mass spectrometry and appears to be based on a limited set of structural scaffolds. Genetic analysis has led to a further understanding of the molecular evolution mechanisms presiding over the generation of these combinatorial peptide libraries. Gene duplication and focal hypermutation, which has been described in cone snails, appear to be common mechanisms to venomous mollusks and spiders. Post-translational modifications, fine structural variations and new molecular scaffolds are other potential mechanisms of toxin diversification, leading to the pharmacologically complex cocktails used for predation and defense.     

镍-金属氢化物电池中的几个物理问题

镍－金属氢化物（Ｎｉ－ＭＨ）电池是贮氢全金研制成功之后的产物。新的高性能贮氢合金的研制是提高Ｎｉ－ＭＨ电池性能的关键之一。文章对贮氢合金的贮氢机制,如贮氢原理,从表面吸附、渗透、体内扩散、相变及其可逆过程,不仅从化学而且从物理学方面作了说明。同时也讨论了贮氢材料的宏观、微观结构对性能的影响,并提出了一个些值得进一步探讨的问题。     

Structural, electronic, and chemical properties of nanoporous carbon

Nanoporous carbon (NPC) exhibits unexplained chemical properties, making it distinct from other graphenelike materials, such as graphite, fullerenes, or nanotubes. In this Letter, we analyze the properties of NPC in terms of its structural motifs, which are derived from defects in distorted graphene sheets. Our density-functional theory calculations show that these motifs can be present in high concentration (up to 1%). Some of them induce localized levels close to the Fermi level, therefore leading to local charging and controlling the material's chemical function, for example, as a catalyst.     

Combinatorial fabrication and screening of organic light-emitting device arrays

The combinatorial fabrication and screening of 2-dimensional (2-d) small molecular UV-violet organic light-emitting device (OLED) arrays, 1-d blue-to-red arrays, 1-d intense white OLED libraries, 1-d arrays to study Förster energy transfer in guest-host OLEDs, and 2-d arrays to study exciplex emission from OLEDs is described. The results demonstrate the power of combinatorial approaches for screening OLED materials and configurations, and for studying their basic properties.     

Sequence-selective nonmacrocyclic two-armed receptors for peptides

Summary Tweezer-like receptor molecules have proven their potential for molecular recognition on several occasions. We decided to make twofold use of this receptor design: firstly to learn whether simple molecular forceps consisting of two peptide chains linked by a spacer are able to selectively bind to small peptides, and secondly to investigate the importance of structural preorganization for the characteristics of the receptors. We prepared two encoded combinatorial libraries based on this design, featuring two combinatorial tripeptide chains held by different scaffolds: the use of chenodeoxycholic acid as spacer provided a rigid scaffold for the forceps, whereas linking the peptide chains by a pentamethylene chain yielded a very flexible forceps structure. Molecules from the cholic acid library recognize and discriminate various enkephalins with micromolar affinities. Molecules from the flexible library show distinct interactions with the enkephalins as well, but the specificity and affinity are clearly diminished. Thus, although the interactions of molecular forceps with peptides are not crucially dependent on structural preorganization, receptors with a rigid design are clearly superior to flexible molecular forceps. Supplementary Material comprising procedures for the preparation and spectroscopical data of compounds5 through8, as well as a listing of the 104 decoded sequences from the assay of the flexible library with⁵Leu-enkephalin/Disperse Red, can be obtained from the author on request.     

Libraries from libraries: Generation and comparison of screening profiles

Summary A positional scanning tetrapeptide library was chemically modified through alkylation and/or reduction of the amide bonds, thus generating three new combinatorial libraries with physico-chemical properties very different from the parent peptide library (libraries from libraries). Specific results were obtained with each of these libraries upon screening in -opioid receptor binding and microdilution antimicrobial assays, illustrating the potential of the libraries from libraries concept for the efficient generation of a variety of chemically diverse combinatorial libraries.     

High throughput combinatorial screening of semiconductor materials

This article provides an overview of an advanced combinatorial material discovery platform developed recently for screening semiconductor materials with properties that may have applications ranging from radiation detectors to solar cells. Semiconductor thin-film libraries, each consisting of 256 materials of different composition arranged into a 16×16 matrix, were fabricated using laser-assisted evaporation process along with a combinatorial mechanism to achieve variations. The composition and microstructure of individual materials on each thin-film library were characterized with an integrated scanning micro-beam x-ray fluorescence and diffraction system, while the band gaps were determined by scanning optical reflection and transmission of the libraries. An ultrafast ultraviolet photon-induced charge probe was devised to measure the mobility and lifetime of individual thin-film materials on semiconductor libraries. Selected results on the discovery of semiconductors with desired band gaps and transport properties are illustrated.     

Chemical synthesis of TASP arrays and their application in protein design

A combinatorial synthesis of de novo proteins is described. The concept of template-assembled synthetic proteins (TASP) has been adapted to an orthogonal assembly of small libraries of purified peptide building blocks. It is combined with the spot synthesis of peptides which is exploited to array cyclic decapeptide templates on cellulose membranes. A cleavable linker on the cellulose allows control of the synthesis. The hydrophilic proteins are constructed by successive cleavage of orthogonal protecting groups on the template, followed by coupling of amphipathic helices in a predefined orientation and finally by incorporation of a cofactor. Libraries of peptides with variation of the amino acids expected to be close to the cofactor were coupled to the cellulose-bound template in all combinations, yielding up to 500 variants of a protein. Cofactors have been inserted either at non-covalent binding sites as heme and Cu2+ or by covalent modification of amino acids as Ru-bipyridine or flavin. The proteins were screened by recording their UV-vis spectra directly on the solid support. The properties screened include the redox potential of heme proteins, charge transfer bands indicating the ligation of Cu-centers, enzymatic activity, and folding stability. Synthesis of the best hits as soluble variants was used for detailed characterization. Iterative improvement in a second screening cycle was efficient in finding novel copper proteins. We discuss the prospects of synthesizing proteins by extending the concept to beta-sandwich proteins and construction of efficient peptide libraries with computer-supported design, as well as the possible usage of improved solid phase materials.     

Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin

Summary Libraries of random-sequence polypeptides have been shown to be valuable sources of novel molecules possessing a variety of useful biologic-like activities, some of which may hold promise as potential vaccines and therapeutics. Previous random peptide expression systems were limited to low levels of peptide production and often to short sequences. Here we describe a series of libraries designed for increased polypeptide length. Cloned as carboxy-terminal extensions of ubiquitin, the fusions were produced inE. coli at high levels, and were purified to homogeneity. The majority of the extension proteins examined could be cleaved from ubiquitin by treatment with a ubiquitin-fusion hydrolase. The libraries described here are appropriate sources of novel polypeptides with desired binding or catalytic function, as well as tools with which to examine inherent properties of proteins as a whole. Toward the latter goal, we have examined structural properties of random-sequence proteins purified from these libraries. Quite surprisingly, fluorescence emission spectra of intrinsic tryptophan residues in several purified fusion proteins, under native-like and denaturing conditions, often resemble those expected for folded and unfolded states, respectively. The results presented here detail an important expansion in the range of potential uses for random-sequence polypeptide libraries.     

A fast method to diagnose phase transition from amorphous to microcrystalline silicon

A series of hydrogenated silicon thin films were prepared by the radio frequency plasma enhanced chemical vapor deposition method (RF-PECVD) with various silane concentrations. The influence of silane concentration on structural and electrical characteristics of these films was investigated to study the phase transition region from amorphous to microcrystalline phase. At the same time, optical emission spectra (OES) from the plasma during the deposition process were monitored to get information about the plasma properties, Raman spectra were measured to study the structural characteristics of the deposited films. The combinatorial analysis of OES and Raman spectra results demonstrated that the OES can be used as a fast method to diagnose phase transition from amorphous to microcrystalline silicon. At last the physical mechanism, why both OES and Raman can be used to diagnose the phase transition, was analyzed theoretically.     

Microscopical and physical characterization of microwave and microwave-hydrothermal synthesis products

Application of microwave energy for materials processing is emerging as an innovative technology with many advantages over the conventional processing, and the rapid progress in this field suggests that microwave material processing (e.g., microwave and microwave-hydrothermal process) will play an outstanding role in the broad field of nanoscience and nanotechnology. This review article gives an up-to-date overview of the current microscopical and physical characterization of the products synthesized by microwave and microwave-hydrothermal process, particularly for oxide nanomaterials because they are indispensable for nanotechnological innovations due to their combinations of infinite variety of structural motifs and properties with manifold morphological features. Basic principles, advantages, and limitations of microwave and microwave-hydrothermal processes are first introduced, and then their recent applications in the synthesis of different classes of functional materials especially for oxide nanomaterials are critically reviewed. Next, the recent progress on the structural and physical characterizations is summarized and discussed. Finally, prospects for future researches within this field are elaborated.