Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues

Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.     

A one-pot synthesis of novel sugar derived 5,6-dihydro-quinazolino[4,3-b]quinazolin-8-ones: an entry towards highly functionalized sugar-heterocyclic hybrids

An efficient and practical one-pot method for the synthesis of novel diversified sugar derived dihydro-quinazolino[4,3-b]quinazolin-8-ones has been reported. Various protected sugar hemiacetals were used to synthesize the hybrid tetracyclic ring system. The one-step reductive transformation of 2-(2-nitrophenyl)-3H-quinazolin-4-one with different sugar hemiacetals furnished the desired tetracyclic product in good yields and with high purity.     

Binding constant measurement by hyper-Rayleigh scattering: bilirubin-human serum albumin binding as a case study

In this paper, a new application of the hyper-Rayleigh scattering technique in determining multiple binding constants of a small molecule like bilirubin to a macromolecule like the protein human serum albumin has been demonstrated. Human serum albumin has two binding sites for bilirubin, and the binding constants have been measured by carrying out a second harmonic titration of the protein against bilirubin and vice versa. The measured binding constants K(1) = 1.5 +/- 0.43 x 10(7) M(-1) and K(2) = 1.01 +/- 0.16 x 10(6) M(-1) agree well with the reported values obtained by other methods.     

Oligosaccharides through reactivity tuning: convergent synthesis of the trisaccharides of the steroid glycoside Sokodoside B isolated from marine sponge Erylus placenta

Chemical synthesis of the trisaccharide of the steroid glycoside Sokodoside B isolated from Erylus placenta is reported. Stereoselective, high-yielding glycosylation strategies through thioglycoside activation using H₂SO₄ immobilized on silica in conjunction with N-iodosuccinimide are used for better results. A late stage TEMPO-mediated oxidation was performed for the formation of required uronic acid moiety. An analog of the target trisaccharide is also prepared by using a bis-glycosylation approach.     

Design and construction of an open multistranded beta-sheet polypeptide stabilized by a disulfide bridge

The design and characterization of an open eight-stranded beta-sheet in a synthetic, 2-fold symmetric 70-residue peptide is described. The design strategy involves the generation of a 35-residue four-stranded beta-sheet peptide in which successive hairpins are nucleated by appropriately positioned (D)Pro-Xxx sequences. Oxidative dimerization using a single Cys residue positioned at the center of the C-terminal strand results in a disulfide-bridged eight-stranded structure. Nuclear Overhauser effects firmly establish an eight-stranded beta-sheet in methanol. In water, the outer strands are frayed, but a well-defined four-stranded beta-sheet stabilized by a disulfide bridge and a hydrophobic cluster is determined from NMR data. Comparison of the precursor peptide with the disulfide-bridged dimer reveals considerable enhancement of beta-sheet content in the latter, suggesting that the disulfide cross-link is an effective strategy for the stabilization of beta-sheets.     

Comparitive study of the sample decomposition procedures in the determination of trace and rare earth elements in anorthosites and related rocks by ICP-MS

ICP-MS has been used for the determination of over 30 geochemically significant trace elements (Sc, V, Cr, Co, Ni, Cu, Zn, Ga, Rb, Sr, Y, Zr, Nb, Cs, Ba, Hf, Ta, Pb, Th, U and REEs) in anorthosites and related rock reference samples. Open acid digestion, pressure decomposition using HF, HNO₃ and HClO₄, and a fusion method using lithium metaborate and subsequent dissolution in dil. HNO₃ were adopted for the decomposition of these rock samples before analysis. The dissolution problems and interference effects are discussed. Rh and Bi were used as internal standards. The first set of data on several rare earths and other trace elements in the Russian anorthosite reference sample, MO-6 are presented along with data on other samples. The data are compared with the available data. The results obtained with different dissolution methods were found to be in good agreement for the majority of the trace elements. The accuracy and precision achieved (better than 6% RSD in most cases) suggested that the data obtained by ICP-MS for such samples are best suited for geochemical interpretations.     

Relative reactivities of glycerophosphates towards permanganate in perchloric acid medium

Summary The reactivities of - and -glycerophosphates towards MnO ₄ ^– in HClO₄ medium have been examined. The reactions between glycerophosphates and MnO ₄ ^– are first order with respect to [glycerophosphate], [MnO ₄ ^– ] and [H⁺]. There is no evidence for cleavage of the C–O–P bond rather than the terminal –CH₂OH group being oxidized to the respective phosphoglyceraldehyde.     

Nonlinear ion transport in liquid and solid electrolytes

This paper describes nonlinear ion transport properties of liquid and solid electrolytes. Typically, the relation between ionic current density and electric field becomes nonlinear at electric fields above 50–100?kV/cm. We review the 1st and 2nd Wien effect found in classical strong and weak electrolyte solutions as well as the strong nonlinear ion transport effects observed for inorganic glasses and for polymer electrolytes. Furthermore, we give an overview over models describing nonlinear ion transport in electrolyte solutions, in glasses and in polymers. Recent results are presented for the nonlinear ionic conductivity of supercooled ionic liquids. We show that supercooled ionic liquids exhibit anomalous Wien effects, which are clearly distinct from the classical Wien effects. We also discuss the frequency dependence of higher-order conductivity and permittivity spectra of these liquids.     

Radiation effect on optimum design analysis of a constructal T-shaped fin with variable thermal conductivity

A constructal T-shaped fin with temperature dependent thermal conductivity of fin the material exposed to both convective and radiative environments is analyzed by Adomian decomposition method. This method provides a closed form of analytical solution for analyzing the temperature distribution, performance and optimum design. A comparative study has been executed among the present and published works. Unlike the published work, dependent parameters on the performance and optimization analysis are highlighted.