Peptide mimics for structural features in proteins. Crystal structures of three heptapeptide helices with a C-terminal 6-->1 hydrogen bond.

The crystal structure determination of three heptapeptides containing alpha-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6-->1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z = 1, a = 9.903 A, b = 10.709 A, c = 11.969 A, alpha = 102.94 degrees, beta = 103.41 degrees, gamma = 92.72 degrees, R = 4.55%; (II) space group P21, Z = 2, a = 10.052 A, b = 17.653 A, c = 13.510 A, beta = 108.45 degrees, R = 4.49%; (III) space group P1, Z = 2 (two independent molecules IIIa and IIIb in the asymmetric unit), a = 10.833 A, b = 13.850 A, c = 16.928 A, alpha = 99.77 degrees, beta = 105.90 degrees, gamma = 90.64 degrees, R = 8.54%. In all cases the helices form 3(10)/alpha-helical (or 3(10)helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (hL) conformation with positive phi, psi values, resulting in 6-->1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4-->1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices proteins, with the terminal pi-type turn being formed by four residues adopting the hRhRhRhL conformation.

Hydration and distortion of peptide helices in crystals. α-Helical structure of a dodecapeptide, Boc-(Ala-Leu-Aib)4-OMe

The dodecapeptide Boc-(Ala-Leu-Aib)(4)-OMe crystallized with two independent helical molecules in a triclinic cell. The two molecules are very similar in conformation, with a 3(10)-helix turn at the N-terminus followed by an alpha-helix, except for an elongated N(7)...O(3) distance in both molecules. All the helices in the crystal pack in a parallel motif. Eleven water sites have been found in the head-to-tail region between the apolar helices that participate in peptide-water hydrogen bonds and a network of water-water hydrogen bonds. The crystal parameters are as follows: 2(C58H104N12O15)+ca. 10H(2)O, space group P1 with a = 12.946(2), b = 17.321(3), c = 20.465(4) Angstrom, alpha = 103.12(2), beta = 105.63(2), gamma = 107.50(2)degrees, Z = 2, R = 10.9% for 5152 data observed > 3 sigma(F), resolution 1.0 Angstrom. In contrast to the shorter sequences [Karle et al. (1988)Proc. Natl. Acad. Sci. USA 85, 299-303] and Boc-(Ala-Leu-Aib)(2)-OMe [Karle et al. (1989) Biopolymers 28, 773-781], no insertion of a water molecule into the helix is observed. However, the elongated N---O distance between Ala(7) NH and Aib(3) CO in both molecules (molecule A, 3.40 Angstrom; molecule B, 3.42 Angstrom) is indicative of an incipient break in the helices. (C) Munksgaard 1994.

Crystal structures of a nonapeptide helix containing alpha,alpha-di-n-butylglycine (Dbg), Boc-Gly-Dbg-Ala-Val-Ala-Leu-Aib-Val-Leu-OMe

Two crystals structures of a nonapeptide (anhydrous and hydrated) containing the amino acid residue alpha, alpha-di-n-butylglycyl, reveal a mixed 3(10)/alpha-helical conformation. Residues 1-7 adopt phi, psi values in the helical region, with Val(8) being appreciably distorted. The Dbg residue has phi, psi values of -40, -37 degrees and -46, -40 degrees in two crystals with the two butyl side chains mostly extended in each. Peptide molecules in the crystals pack into helical columns. The crystal parameters are C50H91N9O12, space group P2(1), with a = 9.789(1) Angstrom, b = 20.240(2) Angstrom, c = 15.998(3) Angstrom, beta = 103.27(1); Z = 2, R = 10.3% for 1945 data observed >3 sigma(F) and C50H91N9O12. 3H(2)O, space group P2(1), with a = 9.747(3) Angstrom, b = 21.002(8) Angstrom, c = 15.885(6) Angstrom, beta = 102.22(3)degrees, Z = 2, R = 13.6% for 2535 data observed >3 sigma(F). The observation of a helical conformation at Dbg suggests that the higher homologs in the alpha, alpha-dialkylated glycine series also have a tendency to stabilize peptide helices. (C) Munksgaard 1996.

Conformation of di-n-propylglycine residues (Dpg) in peptides: crystal structures of a type I 'beta-turn forming tetrapeptide and an alpha-helical tetradecapeptide

The crystal structures of two oligopeptides containing di-n-propylglycine (Dpg) residues, Boc-Gly-Dpg-Gly-Leu-OMe (1) and Boc-Val-Ala-Leu-Dpg-Val-Ala-Leu-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe (2) are presented. Peptide 1 adopts a type I' beta-turn conformation with Dpg(2)-Gly(3) at the corner positions. The 14-residue peptide 2 crystallizes with two molecules in the asymmetric unit, both of which adopt alpha-helical conformations stabilized by 11 successive 5 -> 1 hydrogen bonds. In addition, a single 4 -> 1 hydrogen bond is also observed at the N-terminus. All live Dpg residues adopt backbone torsion angles (phi, psi) in the helical region of conformational space. Evaluation of the available structural data on Dpg peptides confirm the correlation between backbone bond angle N-C-alpha-C' (tau) and the observed backbone phi,psi values. For tau > 106 degrees, helices are observed, while fully extended structures are characterized by tau < 106 degrees. The mean r values for extended and folded conformations for the Dpg residue are 103.6 degrees +/- 1.7 degrees and 109.9 degrees +/- 2.6 degrees, respectively. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Structural and photoelectrical characterization of hot wall deposited CuInSe2 thin films and the fabrication of CuInSe2 based solar cells

Films of CuInSe2 were deposited onto glass substrates by a hot wall deposition method using bulk CuInSe2 as a source material. All the deposited CuInSe2 films were found to be polycrystalline in nature exhibiting the chalcopyrite structure with the crystallite orientation along (101),(112),(103),(211),(220),(312) and (400) directions. The photocurrent was found to increase with increase in film thickness and also with increase of light intensity. Photocurrent spectra show a peak related to the band-to-band transition. The spectral response of CuInSe2 thin films was studied by allowing the radiation to pass through a series of interference filters in the wavelength range 700-1200 rim. Films of higher thickness exhibited higher photosensitivity while low thickness films exhibited moderate photosensitivity. CuInSe2-based Solar cells with different types of buffer layers such as US, Cdse, CuInSe2 and CdSe0.7Te0.3 were fabricated. The current and voltage were measured using an optical power meter and an electrometer respectively. The fabricated solar cells were illuminated using 100 mW/cm(2) white light under AM1 conditions. (C) 2006 Elsevier Inc. All rights reserved.

A new approach to the study of non-linear non-autonomous systems

In this paper, a new approach to the study of non-linear, non-autonomous systems is presented. The method outlined is based on the idea of solving the governing differential equations of order n by a process of successive reduction of their order. This is achieved by the use of “differential transformation functions”. The value of the technique presented in the study of problems arising in the field of non-linear mechanics and the like, is illustrated by means of suitable examples drawn from different fields such as vibrations, rigid body dynamics, etc.

The vibration spectrum of rutile

The long-wave lattice dynamics of rutile has been studied using a rigid ion model. The vibration frequencies for the zero wavevector have been calculated using the expressions for the frequencies of the normal modes derived group theoretically. The observed Raman and infrared frequencies have been explained.

Infrared absorption studies on some derivatives of xanthic, dithiocarbamic and trithiocarbonic acids

The infrared absorption spectra of some of the derivatives of xanthic Image dithiocarbamic Image and trithiocarbonic Image acids are studied in the sodium chloride optics region and the bands assigned to group frequencies. The position of C---O---C and C=S bands in the derivatives of xanthic acid has been discussed from theoretical and experimental evidences and it is suggested that the two strong bands around 1200 and 1030 cm−1 are due to the Image group. The bands around 980 and 1050 cm−1 in the derivatives of dithiocarbamic and trithiocarbonic acids respectively have been assigned to C=S group frequencies. These bands shift to lower frequency in the corresponding ionic compounds while the bands around 1030 and 1200 cm−1 in the ionic compounds of xanthic acid shift to higher and lower frequencies respectively.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structuralvariations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

Intracellular distribution of coenzyme Q in rat liver

Coenzyme Q was found to be distributed in rat liver cell fractions. Mitochondria accounted for only 40–60% of the total. The presence of coenzyme Q in nuclei, isolated by several methods, could always be correlated with the presence of oxidative enzymes. It has been established that coenzyme Q is a constituent of microsomes. Administered coenzyme Q10-C14 was preferentially taken up by mitochondrial and microsomal fractions. Exogenous coenzyme Q appears to be rapidly metabolized.

The Raman spectrum of boric acid

The Raman spectrum of crystalline boric acid is recorded using mercuryλ2537 excitation. Fifteen Raman lines, three of them belonging to the lattice spectrum, are reported. Satisfactory assignments of all the observed Raman frequencies are made using the available X-ray crystal structure data. From the presence of a new high frequency Raman band at about 3420 cm.−1 it is suggested that there might be a small number of long, weak O-H....O hydrogen bonds in the crystal, in addition to the hydrogen bonds of moderate strength reported from X-ray diffraction data.

1-[2,4,6-Trimethyl-3,5-bis(4-oxopiperidin ylmethyl) benzyl ]piperidin- 4-one

In the structure of the title compound, C27H39N3O3, each of the (4-oxopiperidin-1-yl)methyl residues adopts a flattened chair conformation (with the N and carbonyl groups being oriented to either,side of the central C-4 plane) and they occupy positions approximatelym orthogonal to the central benzene ring [C-benzene-C-C-methylene-N torsion angles 103.4 (2), -104.4 (3) and 71.9 (3)degrees]; further, two of these residues are oriented to one side of the central benzene ring with the third to the other side. In the crystal packing, supramolecular layers in the ab plane are sustained by C-H center dotcenter dot center dot O interactions.