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Appropriate positioning and the judicious choice of nearby amino acid residues are demonstrated to lead to >900-fold differences in reactivity of otherwise identical functional groups in short peptides. The described ribosomes and nonribosomal peptide synthetases active site models do not approach the efficiencies of natural enzymes.

The crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and parallel or antiparallel crystal structures of several related peptide sequences are analyzed and described. Results reveal that substitution of a single solvent-exposed residue enabled the parallel coiled-coli tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for the subtle sequence changes to have important structural consequences.

A study was conducted in which internal cavities of different sizes and polarities were characterized in a series of parallel and antiparallel coiled-coil tetramers. These three-dimensional structures illustrate some of the varied surfaces that can be constructed in closely related peptides with very similar overall folds and may provide a basis for the future design of de novo helical proteins.

The effectiveness of the heterocyclic peptide backbone alterations in the plan of a novel means of self-assembling peptide nanotube is discussed which joins the compositional features and has the ability to perform on its outer surface. There are various benefits in utilizing the macrocycles dependent on peptide for nanotube assembly.

It has been possible to design and evaluate a synthetic peptide able to ligate two shorter fragments with considerable efficiency and selectivity. This is the first example of a peptide catalyst with designed substrate binding sites which can substantially speed up a bimolecular reaction.

Experimental evidence shows that the Met -> Nle derivative of the N-terminal domain of the capsid protein cleavage product of the flock house virus efficiently causes the formation of the interdigitated gel phase of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) layers. This is evident in in situ scanning force microscopy of solid supported bilayers and fluorescence spectroscopy of peptide-treated DPPC vesicles. A mechanistic model for the peptide-mediated induction of interdigitation in DPPC bilayers is described.

A study was conducted to clearly characterize some of the structural factors governing the supramolecular organization of the three cyclic peptides belonging to the class of self-assembling peptide nanotubes. The experiment was performed by using grazing incidence X-ray diffraction of Langmuir films of the peptides. Grazing incidence X-ray diffraction and scanning force microscopy were also used to observe the effect of the phospholipid L-alpha-phosphatidic acid dipalmitoyl on the aggregation behavior of two of the peptides.

A porous silicon biosensor using p-type silicon wafers, has been fabricated, and characterized. The transparent porous silicon thin films provided a broad range of pore sizes, and scanning force microscopy and scanning electron microscopy were used to characterize them. The porosity and thickness of the porous layer were determined using reflectance interference spectroscopy and effective medium approximations. The porous silicon matrixes were used in the study of specific protein-ligand binding interactions.

Hollow tubular structures with nanometer-sized interiors or nanotubes are well precedented in both natural and artificial systems. A study was conducted to explore the scope and limitations of a method to promote the biomaterial-based self-assembly of 20 cyclic peptides, which were used to . prepare peptide nanotubes through a selective integration of N-methylated residues, thereby constraining self-assembly to the formation of hydrogen-bonded dimers. The results are discussed.

Research was conducted to examine oriented self-assembly of cyclic peptide nanotubes in lipid membranes. This is the first detailed biophysical investigation of the peptide nanotubes within the context of the lipid film to yield a quantitative estimate of their angle of orientation relative to the lipid bilayer. Results indicate that the orientation of the tubes can be mediated by a supporting environment, implicating biological and nanotechnological applications.

A study was conducted on a new class of self-assembling transmembrane ion channels based on cyclic Beta3-peptides. Liposome-based proton transport assays indicate that Beta3-HTrp residues of channel-forming peptides cyclo[(-Beta3-HTrp)4-] and cyclo[(-Beta3-HTrp-Beta-HLeu)2-] play a key role in solubilizing peptides and allowing their incorporation into lipid membranes. Moreover, the results suggest that the indole NH moiety of Beta3-HTrp may help orient subunits at the lipid-water interface.

An approach based on the self-assembly of flat ring-shaped cyclic peptides into tubular channels in the organosulfur self-assembled monolayers on gold films has proved useful in the design, synthesis and characterization of an unusual diffusion-limited size-selective ion sensor. Grazing angle FTIR spectroscopy has been used to assess the structural properties of monolayer-supported peptide nanotubes. It was also possible to use cyclic voltammetry and impedance spectroscopy to investigate their selective ion transport activities.

Thiol additives act as fast catalysts to the formation of polypeptide chains in native chemical ligation. The transthioesterification process has been successfully used to synthesise several peptide-alpha-thioesters such as phospholipase A2. Weakly activated thioesters are manufactured in a chemical reaction using peptide-alpha-thiocarboxylate and an alkyl halide like benzyl bromide. Peptide-alpha-thiocarboxylate activity is regulated using thiol reducing agent.

A study has been conducted to describe the peptide self-assembly process by using design principles that are unique for nanotubular structures. The peptide nanotubes were constructed by the self-assembly of flat, ring-shaped peptide subunits that consist of alternating D- and L-amino acid residues. The constructs were held together by intersubunit hydrogen bonds while the crystal structures were held by intertubular hydrophobic packing interactions.

A molecular dynamics simulation analysis on self-assembled a peptide nanotube in water shows that water diffusion represents hops between zones which cause transient local deviation from the suitable number of water molecules in an area. The diffusion in the tube may be increased in a way similar to the enhanced conductivity of an n-type semiconductor due to doping. The tubular construct maintains its structural unity during simulations with only few damages at the periphery.

The generation of a large and topologically predetermined protein tertiary structure from a small peptide is demonstrated via a self-organizing process aided by metal ions. Control of the oligomeric state and orientation of peptide subunits involved in the intermolecular assembly process is obtained by taking advantage of the binding energy of a metal ion coordination complex and of the strict geometrical requirements for a strong metal ion-ligand interaction.

A study is conducted to show that the discovery of a biologically active thiostrepton fragment, despite its relatively small size, retains, and in some instances surpasses, the biological properties of the natural substance. The discovery also demonstrates the potential benefits of total synthesis endeavors and the power of complex molecule construction in biology and medicine.

A stable 60-residue artificial four-helix bundle protein was prepared from the Ru(II) metal ion-mediated intermolecular self-assembly of a 15-residue amphiphilic polypeptide containing a pyridyl unit at the N-terminus. The method involved the rearrangement of peptide subunits through metal complexation forming a water-soluble polypeptide molecule. Reactivity and structural analyses were performed to further elucidate the metalloprotein configuration.

The studies on the PCR-independent isothermal molecular translation strategies that function without the need for post-translation purification and which could be implemented with commercially available components are presented. The feasibility of translating small-molecule interactions into nucleic acid outputs are also demonstrated by the utility of a DNA aptamer for translating adenosine into a readily detectable output DNA sequence.

The synthesis and structural and functional analyses of a series of [beta]-amino-acid-containing histone deacetylase (HDAC) inhibitors inspired by cyclic tetrapeptide natural products are described. High-resolution NMR solution structures are determined for a selection of the inhibitors, which have provided many ways of correlating detailed structural information with potency.

The design and functional characterizations of short alpha-helical peptides that mimic the aminoacyl loading and intermodular aminoacyl transfer steps of nonribosomal peptide synthetases (NRPS) with aminolysis rate enhancements in neutral aqueous solutions up to 5400-fold are discussed. The analysis reveals that the helix subunit exchange rates are faster than the rate of intermodular aminoacyl transfer.

The reactions of carbonyl sulfide (COS) are investigated in the context of phosphate activation in neutral aqueous solutions. The results have shown that COS, a simple volcanic gas, can mediate both phosphoryl transfer and peptide synthesis reaction via a single intermediate, aminoacyl N-carboxy-anhydride, under mild aqueous conditions on the prebiotic Earth.

A triazole epsilon2-amino acid can be used as a dipetide surrogate in helical coiled coils and the effects of the substitution on the thermodynamic stability are reported. The epsilon2-amino acid substitution in peptide creates an unusual right-handed interhelical crossover structure such that the helix formed by residues 1-22 of one chain is completed by residues 23-32 of another.

A report that de novo designed synthetic peptide networks can also mimic some of the basic logic functions of the more complex biological networks is presented. It is demonstrated that in response to external stimuli, simple synthetic chemical systems can be designed to express network-dependent logic operations.

The validity of DNA as a specific supramolecular platform for fabrication of molecular logic gates is described. The use of the recognition properties of DNA in creating photonic logic gates capable of AND, NAND, and INHIBIT logic operation is examined.

The design, synthesis, and functional characterization of an intrasterically regulated semisynthetic enzyme is presented. Its application in sequence-specific DNA detection is described.

An attempt made of absolute asymmetric by the repeated asymmetric amplification of the small enantiomeric excess (ee) generated by chance in an initial racemate, which faced problems because they involve novel experimental challenges and probes, and the results found to have implications toward both asymmetric amplification reactions and the origin of biological homochirality, is addressed. The findings suggest caution in interpreting reactions involving large asymmetric amplifications.

Development of transition-metal-catalyzed carbon dioxide (CO2) incorporation reactions into organic molecules, despite it being an important process in organic chemistry, has only a few catalytic synthetic reactions reported. Based on the concept, the reaction is conducted in intramolecular form a nickel-promoted co-oligomerization of bis-1,3-diene and carbon dioxide, and it was found to be an efficient method that helps a catalytic process with extra carbon-carbon bond formation.

The catalytic asymmetric addition of nucleophiles to ketenes is a good way to enhance synthesis of enantioenriched carbonyl derivatives, but for this addition enantiomeric excess as high as eighty percent has to be obtained. The first method for the catalytic enantioselective addition of amines (specifically, pyrroles) to ketenes is developed, and it is demonstrated that the resulting acylpyrroles can be transformed into a broad spectrum of useful derivatives.

Transmembrane channel involved in processes like electrical signaling in nerve as well as muscle cells show ion selectivity as well as rectification are also regulated. A different approach based on self-assembling peptide nanotube architecture especially for the formation of heteromeric synthetic channels is described.

A study was conducted to analyze the de novo design of protein functions. Histidine residues were introduced into the alpha-p sequences at solvent-exposed positions to support attachment sites for redox-active Ru(super III)(NH3)5 moieties. Results indicated that electron-transfer rates consistent with current theory. Findings also showed the possibility of designing functional proteins with reactivity that can be predicted from structure with quantitative accuracy.

The covalent capture process is effectively used for synthesizing a covalently stabilized beta-sheet-like peptide cylinder. A ring shaped peptide subunit is self-assembled to two thermodynamically stable antiparallel beta-sheet-like hydrogen-bonded cylindrical structures via hydrogen bonding interactions. The covalent capture involves the usage of hydrogen-bond-induced 38-member ring forming olefin metathesis in the presence of (Cy3P)2Cl2-Ru=CHCH=CPh2.

Procedures used for the construction of transmembrane ion channels help design artificial transmembrane pore structure exhibiting efficient glucose transport activity across lipid bilayers. Molecular modeling reveals the necessity of the presence of an internal van der Waals pore diameter of greater than 9 angstroms for the transport of glucose via the cylindrical cavity of the tubular transmembrane structure. Kinetic studies reveal that glucose transport due to the addition of channel-forming peptide follows a first-order kinetics.

Adjustment of peptide subunit ring size controls the internal diameter of a peptide nanotube. This technique is used to construct nanotubes with a uniform 13 A Van der Waals pore diameter from a 12-residue cyclic peptide structure. Various spectroscopic techniques and molecular modeling are used to confirm the tubular structure formation.

Cyclic peptides were investigated as molecular adapters for pore forming proteins.

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals. [ABSTRACT FROM AUTHOR]

This article presents a study, which finds heterocyclic peptide backbone modifications in an α-helical coiled coil. Among a number of elegant biomimetic approaches that have been developed for the modification of the peptide backbone, only a few have been applied to protein structures. Here, researchers report high-resolution structural consequences of amide backbone replacements in the context of a folded peptide architecture. The reactivity and functional group tolerance of Cu(I)-catalyzed 1 ,3-dipolar cycloaddition between azides and alkynes to give 1,2,3-triazoles have led to the increasing use of this reaction in bioconjugate chemistry.