Multiple conformational states in crystals and in solution in alpha gamma hybrid peptides. Fragility of the C-12 helix in short sequences

The conformational properties of foldamers generated from alpha gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible coil formational space. This model sequence was anticipated to be a short segment of the alpha gamma C-12 helix, stabilized by three successive 4 -> 1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C-12 hydrogen bonds were obtained at the N-terminus, while a novel C-17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C-9 and C-7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C-12 and C-9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i)<-> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C-12 helix conformation. Lengthening of the (alpha gamma)(n) sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alpha gamma C-12 helix. These results establish that conformational fragility is manifested in short hybrid alpha gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.

Probing Fluorine Interactions in a Polyhydroxylated Environment: Conservation of a C-F center dot center dot center dot H-C Recognition Motif in Presence of O-H center dot center dot center dot O Hydrogen Bonds

Three conformationally locked fluorinated polycyclitols have been specially crafted on a rigid trans-decalin backbone, employing a surprisingly facile pyridine-poly(hydrogen fluoride)-mediated stereospecific epoxide ring opening as the key reaction. Molecula design of the three fluorinated probes under study focused on providing an efficient platform for (a) evaluating the ability of covalently bonded fluorine, vis-a-vis the isosteric hydroxy group, to act as a H-bond acceptor and (b) examining the possibility for an organic fluorine moiety, placed suitably in a spatially invariant position, to engage an 1,3-diaxial OH functionality in a purported intramolecular O-H center dot center dot center dot F hydrogen bond. The present endeavour reveals that C(sp(3))-F center dot center dot center dot H-C(sp(3)) hydrogen bonds, though weak and lesser investigated, can indeed be observed and supramolecular recognition motifs, involving such interactions, can be conserved even in crystal structures laden with stronger O-H center dot center dot center dot O hydrogen bonds.

Plasticity in the primary binding site of galactose/N-acetylgalactosamine-specific lectins - Implication of the C-H center dot center dot center dot O hydrogen bond at the specificity-determining C-4 locus of the saccharide in 4-methoxygalactose recognition by jacalin and winged bean (basic) agglutinin I

It is currently believed that an unsubstituted axial hydroxyl at the specificity-determining C-4 locus of galactose is indispensable for recognition by galactose/N-acetylgalactosamine-specific lectins. Titration calorimetry demonstrates that 4-methoxygalactose retains binding allegiance to the Moraceae lectin jacalin and the Leguminosae lectin, winged bean (basic) agglutinin (WBA I). The binding reactions were driven by dominant favorable enthalpic contributions and exhibited significant enthalpy-entropy compensation. Proton NMR titration of C-methoxygalactose with jacalin and WBA I resulted in broadening of the sugar resonances without any change in chemical shift. The alpha-and beta-anomers of 4-methoxygalactose were found to be in slow exchange with free and lectin-bound states. Both the anomers experience magnetically equivalent environments at the respective binding sites. The binding constants derived from the dependence of NMR line widths on 4-methoxygalactose concentration agreed well with those obtained from titration calorimetry. The results unequivocally demonstrate that the loci corresponding to the axially oriented C-4 hydroxyl group of galactose within the primary binding site of these lectins exhibit plasticity. These analyses suggest, for the first time, the existence of C-H ... O-type hydrogen-bond(s) in protein-carbohydrate interactions in general and between the C-4 locus of galactose derivative and the lectins jacalin and WBA I in particular.

Crystallization and preliminary X-ray studies of the C-terminal domain of Mycobacterium tuberculosis LexA

The C-terminal domain of Mycobacterium tuberculosis LexA has been crystallized in two different forms. The form 1 and form 2 crystals belonged to space groups P3(1)21 and P3(1), respectively. Form 1 contains one domain in the asymmetric unit, while form 2 contains six crystallographically independent domains. The structures have been solved by molecular replacement.

Thermodynamic measurements of b.c.c. Cr-Mn solid solutions at 1373 K

Thermodynamics of Cr-Mn alloys have been studied by Eremenko et al (l) using a fused salt e.m.f.technique. Their results indicate positive deviations from ideality at 1023 K. Kaufman (2) has independently estimated negative enthaipy and excess entropy for the b.c.c. Cr-Mn alloys, such that at high temperatures, the entropy term predominates over the enthalpy term giving positive deviations from ideality. Recently the thermodynamic properties of the alloys have been measured by 3acob (3) using a Knudsen cell technique in the temperature range of 1200 to 1500 K. The results indicate mild negative deviations from ideality over the entire composition range. Because of the differences in the reported results and Mn being a volatile component in the alloys which leads to surface depletion under a dynamic set up, an isopiestic technique is used to measure the properties of the alloys.

Inelastic dynamic response of R.C. beam column joints by using B.E.M.

A BEM formulation to obtain the inelastic response of R.C. Beam-Column joints subjected to sinusoidal loading along the boundary is presented. The equations of motion are written along with kinematical and constitutive equations. The dynamic reciprocal theorem is presented and the temporal dependence is removed by assuming steady state response.

Probing the role of the C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val- (D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all L analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed a-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-(HO)-O-... hydrogen bond between residue 4 (CH)-H-alpha and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C-alpha atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt at conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-(HO)-O-... hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

MNDO study of coupled strained hydrocarbons: Additivity of exocyclic C---C bond contraction induced by different ring systems

MNDO geometry optimizations were carried out on a series of symmetrically and unsymmetrically coupled strained ring hydrocarbons, R1-R1 and R1–R2 (R1=methyl, cyclopropyl, 1-bicyclo[1.1.0]butyl, 1-bicyclo[1.1.1]pentyl, prismyl, cubyl, 6-tricyclo [3.1.1.03,6]heptyl, and tetrahedryl groups; R2=methyl and cyclopropyl). The remarkable contraction of the C---C bond connecting the strained rings found experimentally in a few cases was reproduced correctly by the calculations. A linear correlation was found between the bond length shortening and the bond angle widening at the corresponding carbon atoms for all the structures considered. The reduction in C---C bond lengths due to various ring systems is additive. The additivity indicates that inter-ring interactions which effect the central bond length are absent and confirms the common electronic origin of bond contraction in these systems, viz. enhanced s-character in the exocyclic bonds of strained rings.

Ultimate Strength of R.C. Wall Panels in Two-Way In-Plane Action

Test results of 24 reinforced concrete wall panels in two-way action (i.e., supported on all the four sides) and subjected to in-plane vertical load are presented. The load is applied at an eccentricity to represent possible accidental eccentricity that occurs in practice due to constructional imperfections. Influences of aspect ratio, thinness ratio, slendemess ratio, vertical steel, and horizontal steel on the ultimate load are studied. Two equations are proposed to predict the ultimate load carried by the panels. The first equation is empirical and is arrived at from trial and error fitting with test data. The second equation is semi-empirical and is developed from a modification of the buckling strength of thin rectangular plates. Both the equations are formulated so as to give a safe prediction of a large portion of ultimate strength test results. Also, ultimate load cracking load and lateral deflections of identical panels in two-way action (all four sides supported) and oneway action (top and bottom sides only supported) are compared.

Functions Of Cytochrome-C In Regulation Of Electron-Transfer And Protein Folding

Cytochrome c, a "mobile electron carrier" of the mitochondrial respiratory chain, also occurs in detectable amounts in the cytosol, and can receive electrons from cytochromes present in endoplasmic reticulum and plasma membranes as well as from superoxide and ascorbate. The pigment was found to dissociate from mitochondrial membranes in liver and kidney when rats were subjected to heat exposure and starvation, respectively. Treating cytochrome c with hydroxylamine gives a partially deaminated product with altered redox properties; decreased stimulation of respiration by deficient mitochondria, increased reduction by superoxide, and complete loss of reducibility by plasma membranes. Mitochondria isolated from brown adipose tissue of cold-exposed rats are found to be sub-saturated with cytochrome c. The ability of cytochrome c to reactivate reduced ribonuclease is now reinterpreted as a molecular chaperone role for the hemoprotein.

Inhibition of hepatitis C virus replication by herbal extract: Phyllanthus amarus as potent natural source

Hepatitis C virus infection is a major health problem worldwide. Developing effective antiviral therapy for HCV is the need of the hour. The viral enzymes NS3 protease and NS5B RNA dependent RNA polymerase are essential enzymes for polyprotein processing and viral RNA replication and thus can be potential targets for screening anti-HCV compounds. A large number of phytochemicals are present in plants, which are found to be promising antiviral agents. In this study, we have screened inhibitory effect of different plant extracts against the NS3 and NS5B enzymes of hepatitis C virus. Methanolic extracts were prepared from various plant materials and their inhibitory effects on the viral enzymes were determined by in vitro enzyme assays. Effect on viral RNA replication was investigated by using TaqMan Real time RT-PCR. Interestingly, Phyllanthus amarus root (PAR) extract showed significant inhibition of HCV-NS3 protease enzyme; whereas P. amarus leaf (PAL) extract showed considerable inhibition of NS5B in the in vitro assays. Further, the PAR and PAL extracts significantly inhibited replication of HCV monocistronic replicon RNA and HCV H77S viral RNA in HCV cell culture system. However, both PAR and PAL extracts did not show cytotoxicity in Huh7 cells in the MTT assay. Furthermore, addition of PAR together with IFN-alpha showed additive effect in the inhibition of HCV RNA replication. Results suggest the possible molecular basis of the inhibitory activity of PA extract against HCV which would help in optimization and subsequent development of specific antiviral agent using P. amarus as potent natural source. (C) 2011 Elsevier B.V. All rights reserved.

A study of Al2O3:C films on Si(100) grown by low pressure MOCVD

We report the characterization of carbonaceous aluminium oxide, Al2O3:C, films grown on Si(100) by metalorganic chemical vapor deposition. The focus is on the study of the effects of carbon on the dielectric properties of aluminium oxide in a qualitative manner. The carbon present in the aluminium oxide film derives from aluminium acetylacetonate used as the source of aluminium. As-grown films comprise nanometer-sized grains of alumina (∼ 20–50 nm) in an amorphous carbonaceous matrix, as examined by X-ray diffractometry (XRD) and transmission electron microscopy (TEM). The films are shiny; they are smooth as observed by scanning electron microscopy (SEM). An attempt has been made to explore the defects (viz., oxide charge density) in the aluminium oxide films using room temperature high frequency capacitance – voltage (C-V) and current–voltage (I-V) measurements. The hysteresis and stretch-out in the high frequency C-V plots is indicative of charge trapping. The role of heteroatoms, as characterized by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy, in the transport of charge in Al2O3:C films is discussed.