Hydrogen bonding in peptide helices - Analysis of two independent helices in the crystal structure of a peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe

The crystal structure determination of the heptapeptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe reveals two peptide helices in the asymmetric unit, Crystal parameters are: space group P2(1), a = 10.356(2) Angstrom, b = 19.488(5) Angstrom, c = 23.756(6) Angstrom, beta = 102.25(2)degrees), V = 4685.4 Angstrom(3), Z = 4 and R = 5.7% for 7615 reflections [I>3 sigma(I)]. Both molecules adopt largely alpha-helical conformations with variations at the C-terminus, Helix type Is determined by analysing both 4-->1 and 5-->1 hydrogen-bond interactions and comparison with the results of analysis of protein structures. The presence of two 4-->1 hydrogen-bond interactions, besides four 5-->1 interact ions in both the conformations provides an opportunity to characterize bifurcated hydrogen bonds at high resolution, Comparison of the two helical conformations with related peptide structures suggests that distortions at the C-terminus are more facile than at the N-terminus.

Promotion of fibronectin independent invasion by C5a peptidase into epithelial cells in group A Streptococcus

Background & objectives: Group A Streptococcus, causative agent of several clinical manifestations codes for multiple protein invasins which help the bacterium to enter non-phagocytic cells. C5a peptidase (SCPA) is a surface protein conserved among different serotypes of M1 strain. The present study was taken up to study SCPA promoted fibronectin independent entry of GAS into epithelial cells. Methods: An isogenic 90226 emm1DeltaAB (M1(-)) mutant was constructed, with thermosensitive pGhost vector. This isogenic M1(-) mutant expressed SCPA on the surface as determined by Western blotting and immunofluorescence. Results: On preincubation with anti-SCPA serum, the isogenic M1(-) strain exhibited 54 per cent decreased invasion as compared to the bacteria incubated with control serum. Also, purified recombinant SCPA proteins blocked internalization of M1(-) streptococci into HEp-2 cells. The M1(-) strain invaded at the same efficiency in the presence or absence of fibronectin. Interpretation & conclusion: These results suggested that SCPA acted as a potential invasin of group A streptococcus and promoted invasion independent of fibronectin.

Spectral analysis of noise in the neonatal intensive care unit

Objective To perform spectral analysis of noise generated by equipments and activities in a level III neonatal intensive care unit (NICU) and measure the real time sequential hourly noise levels over a 15 day period. Methods Noise generated in the NICU by individual equipments and activities were recorded with a digital spectral sound analyzer to perform spectral analysis over 0.5–8 KHz. Sequential hourly noise level measurements in all the rooms of the NICU were done for 15 days using a digital sound pressure level meter. Independent sample t test and one way ANOVA were used to examine the statistical significance of the results. The study has a 90% power to detect at least 4 dB differences from the recommended maximum of 50 dB with 95 % confidence. Results The mean noise levels in the ventilator room and stable room were 19.99 dB (A) sound pressure level (SPL) and 11.81 dB (A) SPL higher than the maximum recommended of 50 dB (A) respectively (p < 0.001). The equipments generated 19.11 dB SPL higher than the recommended norms in 1–8 KHz spectrum. The activities generated 21.49 dB SPL higher than the recommended norms in 1–8 KHz spectrum (p< 0.001). The ventilator and nebulisers produced excess noise of 8.5 dB SPL at the 0.5 KHz spectrum.Conclusion Noise level in the NICU is unacceptably high. Spectral analysis of equipment and activity noise have shown noise predominantly in the 1–8 KHz spectrum. These levels warrant immediate implementation of noise reduction protocols as a standard of care in the NICU.

Shell-model calculation of defect energies in alkali halides employing crystal-independent interionic potential parameters

Shell model calculation of defect energies in alkali halides have been carried out using the ion-dependent, crystal-independent potential parameters of Sangster and Atwood (1978). Results indicate that appreciable differences exist between barrier heights for migration of cations and anions. While barrier heights for cations are generally lower than for anions in alkali halides of NaCl structure, the opposite is true in alkali halides of CsCl structure.

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Inference for the Component and System Lifetime Distribution of a k-unit Parallel System Based on System Data

In this paper, we consider the inference for the component and system lifetime distribution of a k-unit parallel system with independent components based on system data. The components are assumed to have identical Weibull distribution. We obtain the maximum likelihood estimates of the unknown parameters based on system data. The Fisher information matrix has been derived. We propose -expectation tolerance interval and -content -level tolerance interval for the life distribution of the system. Performance of the estimators and tolerance intervals is investigated via simulation study. A simulated dataset is analyzed for illustration.

Beta-Turn Conformations In Crystal-Structures Of Model Peptides Containing Alpha,Alpha-Di-N-Propylglycine And Alpha,Alpha-Di-N-Butylglycine

The crystal state conformations of three peptides containing the alpha, alpha-dialkylated residues, alpha,alpha-di-n-propylglycine (Dpg) and alpha,alpha-di-n-butylglycine (Dbg), have been established by x-ray diffraction. Boc-Ala-Dpg-Ala-OMe (I) and Boc-Ala-Dbg-Ala-OMe (III) adopt distorted type II beta-turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: phi = 66.2 degrees, psi = 19.3 degrees; III: phi = 66.5 degrees, psi = 21.1 degrees) deviate appreciably from ideal values for the i + 2 residue in a type II beta-turn. In both peptides the observed (N...O) distances between the Boc CO and Ala(3) NH groups are far too long (I: 3.44 Angstrom; III: 3.63 Angstrom) for an intramolecular 4 --> 1 hydrogen bond. Boc-Ala-Dpg-Ala-NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules IIA and IIB adopt consecutive beta-turn (type III-III in IIA and type III-I in IIB) or incipient 3(10)-helical structures, stabilized by two intramolecular 4 --> 1 hydrogen bonds. In all four molecules the bond angle N-C-alpha-C' (tau) at the Dxg residues are greater than or equal to 110 degrees. The observation of conformational angles in the helical region of phi,psi space at these residues is consistent with theoretical predictions.

Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THE SHMT also catalyses several THF-independent side reactions such as cleavage of P-hydroxy amino acids, trans-amination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect oil either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a Mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three Mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

The crystal structure of eulytite Pb3BiV3O12

The crystal structure of Pb3BiV3O12 was solved using single-crystal X-ray diffraction technique. The compound crystallizes in the cubic system View the MathML source (No. 220) with eulytite structure with a = 10.7490(7) Å, V = 1241.95(14) Å3 and Z = 4. The final R1 value of 0.0198 (wR2=0.0384) was achieved for 359 independent reflections during the structure refinement. The Pb2+ and Bi3+ cations occupy the special position (16c) while the oxygen anions occupy the general position (48e) in the crystal structure. Unlike many other eulytite compounds, all the crystallographic positions are fully occupied. The structure consists of edge-shared Pb/Bi octahedra linked at the corners to independent [VO4]3− tetrahedra units, generating a eulytite-type network in the crystal lattice.

Response And Stability Of A Stochastic Beam-Column Using Stochastic Fem

A beam-column resting on continuous Winkler foundation and discrete elastic supports is considered. The beam-column is of variable cross-section and the variation of sectional properties along the axis of the beam-column is deterministic. Young's modulus, mass per unit length and distributed axial loadings of the beam-column have a stochastic distribution. The foundation stiffness coefficient of the Winkler model, the stiffnesses of discrete elastic supports, stiffnesses of end springs and the end thrust, are all considered as random parameters. The material property fluctuations and distributed axial loadings are considered to constitute independent, one-dimension uni-variate homogeneous real stochastic fields in space. The foundation stiffness coefficient, stiffnesses of the discrete elastic supports, stiffnesses of end springs and the end thrust are considered to constitute independent random variables. Static response, free vibration and stability behaviour of the beam-column are studied. Hamilton's principle is used to formulate the problem using stochastic FEM. Sensitivity vectors of the response and stability parameters are evaluated. Using these statistics of free vibration frequencies, mode shapes, buckling parameters, etc., are evaluated. A numerical example is given.

Instabilities and Waves in Thin Films of Living Fluids

We formulate the thin-film hydrodynamics of a suspension of polar self-driven particles and show that it is prone to several instabilities through the interplay of activity, polarity, and the existence of a free surface. Our approach extends, to self-propelling systems, the work of Ben Amar and Cummings [Phys. Fluids 13 1160 (2001)] on thin-film nematics. Based on our estimates the instabilities should be seen in bacterial suspensions and the lamellipodium, and are potentially relevant to the morphology of biofilms. We suggest several experimental tests of our theory.

Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase

Dimeric and monomeric forms of the enzyme triosephosphate isomerase (TIM) from Plasmodium falciparum (Pf) have been detected under conditions of nanoflow by electrospray mass spectrometry. The dimer (M = 55 663 Da) exhibits a narrow charge state distribution with intense peaks limited to values of 18(+) to 21(+), maximal intensity being observed for charge states 19(+) and 20(+). A monomeric species with a charge state distribution ranging from 11(+) to 16(+) is also observed, which may be assigned to folded dissociated subunits. Complete dimer dissociation results under normal electrospray condition. The effects of solution pH and source temperature have been investigated. The observation of four distinct charge state distributions which may be assigned to a dimer, folded monomer, partially folded monomer and unfolded monomer is reported. Circular dichromism and fluorescence studies of Pf TIM at low pH support the retention of substantial secondary and tertiary structures. Satellite peaks in mass spectra corresponding to hydrated species are also observed and isotope shift upon deuteration is demonstrated. The analysis of all available independent crystal structures of Pf TIM and TIMs from other organisms permits identification of structurally conserved water molecules. Hydration observed in the dimer and folded monomeric forms in the gas phase may correspond to these conserved sites.

Spin-state equilibria in the LCoO3 system from 59Co NMR

Spin-state equilibria in the whole set of LCoO3 (where L stands for a rare-earth metal or Y) have been investigated with the use of 59Co NMR as a probe for the polycrystalline samples (except Ce) in the temperature interval 110-550 K and frequency range 3- 11.6 MHz. Besides confirming the coexistence of the high-spin—low-spin state in this temperature range, a quadrupolar interaction of ∼0.1 -0.5 MHz has been detected for the first time from 59Co NMR. The NMR line shape is found to depend strongly on the relative magnitude of the magnetic and quadrupolar interactions present. Analysis of the powder pattern reveals two basically different types of transferred hyperfine interaction between the lighter and heavier members of the rare-earth series. The first three members of the lighter rare-earth metals La, Pr (rhombohedral), and Nd (tetragonal), exhibit second-order quadrupolar interaction with a zero-asymmetry parameter at lower temperatures. Above a critical temperature TS (dependent on the size of the rare-earth ion), the quadrupolar interaction becomes temperature dependent and eventually gives rise to a first-order interaction thus indicating a possible second-order phase change. Sm and Eu (orthorhombic) exhibit also a second-order quadrupolar interaction with a nonzero asymmetry parameter ((η∼0.47)) at 300 K, while the orthorhombic second-half members (Dy,..., Lu and Y) exhibit first-order quadrupolar interaction at all temperatures. Normal paramagnetic behavior, i.e., a linear variation of Kiso with T-1, has been observed in the heavier rare-earth cobaltites (Er,..., Lu and Y), whereas an anomalous variation has been observed in (La,..., Nd)CoO3. Thus, Kiso increases with increasing temperature in PrCoO3 and NdCoO3. These observations corroborate the model of the spin-state equilibria in LCoO3 originally proposed by Raccah and Goodenough. A high-spin—low-spin ratio, r=1, can be stabilized in the perovskite structure by a cooperative displacement of the oxygen atoms from the high-spin towards the low-spin cation. Where this ordering into high- and low-spin sublattices occurs at r=1, one can anticipate equivalent displacement of all near-neighbor oxygen atoms towards a low-spin cobalt ion. Thus the heavier LCoO3 exhibits a small temperature-independent first-order quadrupolar interaction. Where r<1, the high- and low-spin states are disordered, giving rise to a temperature-dependent second-order quadrupolar interaction with an anomalous Kiso for the lighter LCoO3.

M. bovis BCG induced expression of COX-2 involves nitric oxide-dependent and -independent signaling pathways

In a multifaceted immunity to mycobacterial infection, induced expression of cyclooxygenase-2 (COX-2) by Mycobacterium bovis bacillus Calmette-Guerin (BCG) may act as an important influencing factor for the effective host immunity. We here demonstrate that M. bovis BCG-triggered TLR2-dependent signaling leads to COX-2 and PGE2 expression in vitro in macrophages and in vivo in mice. Further, the presence of PGE2 could be demonstrated in sera or cerebrospinal fluid of tuberculosis patients. The induced COX-2 expression in macrophages is dependent on NF-kappa B activation, which is mediated by inducible NO synthase (iNOS)/NO-dependent participation of the members of Notch1-PI-3K signaling cascades as well as iNOS-independent activation of ERK1/2 and p38 MAPKs. Inhibition of iNOS activity abrogated the M. bovis BCG ability to trigger the generation of Notch1 intracellular domain (NICD), a marker for Notch1 signaling activation, as well as activation of the PI-3K signaling cascade. On the contrary, treatment of macrophages with 3-morpholinosydnonimine, a NO donor, resulted in a rapid increase in generation of NICD, activation of PI-3K pathway, as well as the expression of COX-2. Stable expression of NICD in RAW 264.7 macrophages resulted in augmented expression of COX-2. Further, signaling perturbations suggested the involvement of the cross-talk of Notch1 with members with the PI-3K signaling cascade. These results implicate the dichotomous nature of TLR2 signaling during M. bovis BCG-triggered expression of COX-2. In this perspective, we propose the involvement of iNOS/NO as one of the obligatory, early, proximal signaling events during M. bovis BCG-induced COX-2 expression in macrophages.

5,7-Dimethoxy-2-phenyl-4H-chromen-4-one

The asymmetric unit of the title compound, C17H14O4, contains two independent molecules which differ in the relative orientations of the phenyl rings with repect to the essentially planar [maximum deviations of 0.029 (2) and 0.050 (2) angstrom in the two molecules] chromene fused-ring system, forming dihedral angles of 10.3 (5) and 30.86 (5)degrees in the two molecules. The crystal structure is stabilized by weak C-H center dot center dot center dot O and C-H center dot center dot center dot pi interactions, and pi-pi stacking interactions.