Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Support vector machine approach for the switching transient peak overvoltages during line energization

At the time of restoration transmission line switching is one of the major causes, which creates transient overvoltages. Though detailed Electro Magnetic Transient studies are carried out extensively for the planning and design of transmission systems, such studies are not common in a day-today operation of power systems. However it is important for the operator to ensure during restoration of supply that peak overvoltages resulting from the switching operations are well within safe limits. This paper presents a support vector machine approach to classify the various cases of line energization in the category of safe or unsafe based upon the peak value of overvoltage at the receiving end of line. Operator can define the threshold value of voltage to assign the data pattern in either of the class. For illustration of proposed approach the power system used for switching transient peak overvoltages tests is a 400 kV equivalent system of an Indian southern gri

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.

Delay optimal control algorithm for a multiaccess fading channel with peak power constraint

We consider an optimal power and rate scheduling problem for a multiaccess fading wireless channel with the objective of minimising a weighted sum of mean packet transmission delay subject to a peak power constraint. The base station acts as a controller which, depending upon the buffer lengths and the channel state of each user, allocates transmission rate and power to individual users. We assume perfect channel state information at the transmitter and the receiver. We also assume a Markov model for the fading and packet arrival processes. The policy obtained represents a form of Indexability.

The syntheses, characterizations, X-ray crystal structures and properties of Cu(I) complexes of a bis-bidentate schiff base ligand

Bis-bidentate Schiff base ligand L and its two mononuclear complexes [CuL(CH3CN)(2)]ClO4 (1)and [CuL(PPh3)(2)]ClO4 (2)have been prepared and thoroughly characterized by elemental analyses, IR, UV-Vis, NMR spectroscopy and X-ray diffraction analysis. In both the complexes the metal ion auxiliaries adopt tetrahedral coordination environment. Their reactivity, electrochemical and photophysical behavior have been studied. Complex 1 shows reversible Cu-II/I couple with potential 0.74 V versus Ag/AgCl in CH2Cl2. At room temperature L is weakly fluorescent in CH2Cl2, however in Cu(I)complexes 1 and 2 the emission in quenched. (C) 2009 Elsevier B. V. All rights reserved.

Structural plasticity and enzyme action: Crystal structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase

Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacteritan tuberculosis has been determined in three crystal forms. This structure and the structure of the enzyme frorn Escherichia coli in its crystal differ substantially on account of the binding of the C terminus of the E. coli enzyme to the peptide-binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body, of the molecule and a polypepticle Y stretch involving a loop and a helix. This stretch is in the open conformation when the enzyme is in the free state as in the crystals of M. tuberculosis peptidyl-tRNA hydrolase. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the E. coli crystal mimics the peptide-bound enzyme molecule. The peptide stretch referred to earlier now closes on the bound peptide. Concurrently, a channel connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of two residues. Thus, the crystal structure of M. tuberculosis peptidyl-tRNA hydrolase when compared with the crystal structure of the E. coli enzyme, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule. (c) 2007 Elsevier Ltd. All rights reserved.

Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs

Acyl Carrier Protein (ACP) from the malaria parasite, Plasmodium falciparum (PfACP) in its holo form is found to exist in two conformational states in solution. Unique 3D solution structures of holo-PfACP have been determined for both equilibrium conformations, using high-resolution NMR methods. Twenty high-resolution solution structures for each of the two forms of holo-PfACP have been determined on the basis of 1226 and 1218 unambiguously assigned NOEs (including NOEs between 4 '-phosphopantetheine prosthetic group (4 '-PP) and protein), 55 backbone dihedral angles and 26 hydrogen bonds. The atomic rmsd values of the determined structures of two equilibrium forms, about the mean coordinates of the backbone and heavy atoms, are 0.48 +/- 0.09 and 0.92 +/- 0.10 and 0.49 +/- 0.08 and 0.97 +/- 0.11 angstrom, respectively. The interaction of 4 '-PP with the polypeptide backbone is reported here for the first time for any of the ACPs. The structures of holo-PfACP consist of three well-defined helices that are tightly packed. The structured regions of the molecule are stabilized by extensive hydrophobic interactions. The difference between the two forms arises from a reorientation of the 4 '-PP group. The enthalpy difference between the two forms, although small, implies that a conformational switch is essential for the activation of holo-ACP. Sequence and structures of holo-PfACP have been compared with those of the ACPs from type I and type II fatty acid biosynthesis pathways (FAS), in particular with the ACP from rat and the butyryl-ACP from E. coli. The PfACP structure, thus determined has several novel features hitherto not seen in other ACPs.

Suppression of spinel formation to induce reversible thermal behavior in the layered double hydroxides (LDHs) of Co with Al, Fe, Ga, and In

The layered double hydroxides (LDHs) of Co with trivalent cations decompose irreversibly to yield oxides with the spinel structure. Spinel formation is aided by the oxidation of Co(II) to Co(III) in the ambient atmosphere. When the decomposition is carried out under N-2, the oxidation of Co(II) is suppressed, and the resulting oxide has the rock salt structure. Thus, the Co-Al-CO32-/Cl- LDHs yield oxides of the type Co1- Al-x(2x/3)rectangle O-x/3, which are highly metastable, given the large defect concentration. This defect oxide rapidly reverts back to the original hydroxide on soaking in a Na2CO3 solution. Interlayer NO3- anions, on the other hand, decompose generating a highly oxidizing atmosphere, whereby the Co-Al-NO3- LDH decomposes to form the spinel phase even in a N-2 atmosphere. The oxide with the defect rock salt structure formed by the thermal decomposition of the Co-Fe-CO32- LDH under N2, on soaking in a Na2CO3 solution, follows a different kinetic pathway and undergoes a solution transformation into the inverse spinel Co(Co, Fe)(2)O-4. Fe3+ has a low octahedral crystal field stabilization energy and therefore prefers the tetrahedral coordination offered by the structure of the inverse spinel rather than the octahedral coordination of the parent LDH. Similar considerations do not hold in the case of Ga- and In-containing LDHs, given the considerable barriers to the diffusion of M3+ (M=Ga, In) from octahedral to tetrahedral sites owing to their large size. Consequently, the In-containing oxide residue reverts back to the parent hydroxide, whereas this reconstruction is partial in the case of the Ga-containing oxide. These studies show that the reversible thermal behavior offers a competing kinetic pathway to spinel formation. Suppression of the latter induces the reversible behavior in an LDH that otherwise decomposes irreversibly to the spinel.

Quantum phase transition in capacitively coupled double quantum dots

We investigate two equivalent, capacitively coupled semiconducting quantum dots, each coupled to its own lead, in a regime where there are two electrons on the double dot. With increasing interdot coupling, a rich range of behavior is uncovered: first a crossover from spin- to charge-Kondo physics, via an intermediate SU(4) state with entangled spin and charge degrees of freedom, followed by a quantum phase transition of Kosterlitz-Thouless type to a non-Fermi-liquid "charge-ordered" phase with finite residual entropy and anomalous transport properties. Physical arguments and numerical renormalization group methods are employed to obtain a detailed understanding of the problem.

Identification of carbohydrate structures as receptors for localised adherent enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli strains of diffused adherent (DA) and localised adherent (LA) phenotypes were tested for their ability to bind to glycolipids. DA strains did not bind to the glycolipids tested, while LA strains bound to asialo GM1, asialo GM2, globoside and lacto-N-neotetraose in decreasing order of avidity. The minimum common sequence among the four glycolipids could be delineated as GalNac β 1–4 Gal as the binding epitope with GalNac β 1–3 Gal and GlcNac β 1–3 Gal serving as relatively weaker binders. The binding was not inhibited by a variety of free oligosaccharides or by the neoglycoproteins tested. Adhesion-negative mutants of an enteropathogenic LA strain showed a markedly reduced binding to asialo GM1 indicating that the recognition of GalNac β 1–4 Gal was correlated with the ability to adhere to HeLa cells. Thus recognition and binding to glycolipids could play an important role in colonisation through adherence to intestinal surfaces.

Reversible double insertion of aryl isocyanates into the Ti-O bond of titanium(IV) isopropoxide

The insertion of phenyl isocyanate into titanium isopropoxide leads to the formation of a dimeric complex [Ti(O ' Pr)(2)(mu-O ' Pr){C6H5N(O ' Pr)CO}](2) (1) which has been structurally characterized. Reaction of titanium isopropoxide with two and more than 2 equiv. of phenyl isocyanate is complicated by competitive, reversible insertion between the titanium carbamate and titanium isopropoxide. The ligand formed by insertion of phenyl isocyanate into the titanium carbamate has been structurally characterized in its protonated form C6H5N{C(O ' Pr)O}C(O)N(H)C6H5 (3aH). Insertion into the carbamate is kinetically favored whereas insertion into isopropoxide gives the thermodynamically favored product. (c) 2004 Elsevier B.V. All rights reserved.

Large molecular motions are tolerated in crystals of diamine double salt of trans-chlorocinnamic acids with trans-1,2-diaminocyclohexane

Contrary to the general assumption that photoreactions in crystals may not proceed with large molecular motions, a pedal-like motion prompted by electronic excitation is believed to be involved during the β-dimer formation from the crystals of the diamine double salt of trans-2,4-dichlorocinnamic acid and trans-1,2-diaminocyclohexane.

Local structure of Sr(2)FeMoxW1-xO(6) double perovskites studied by EXAFS

Sr2FeMoO6 double perovskits display low field MR at a relatively high temperature and unusual ferromagnetic properties. These compounds depicts metal to insulator transition increasing x above x(c) similar to 0.25. A comparative analysis of the near edge regions (XANES) suggests that iron is Fe3+ in the metallic range. Checking the end compounds, we found that the doped samples can be viewn as inhomogeneous distributions of the end compounds. This could help to distinguish between the two scenarios proposed to explain the metal to insulator transition. Moreover, the local atomic structure of Sr2FeMoxW1-xO6 as a function of composition (0 <= x <= 1) has been investigated by Extended X-ray absorption spectroscopy (EXAFS) a the Fe, Mo, Sr K-edges andW L-III-edge.

Spectroscopy of tissue triglyceride composition : In vitro and in vivo studies

Lipid analysis is commonly performed by gas chromatography (GC) in laboratory conditions. Spectroscopic techniques, however, are non-destructive and can be implemented noninvasively in vivo. Excess fat (triglycerides) in visceral adipose tissue and liver is known predispose to metabolic abnormalities, collectively known as the metabolic syndrome. Insulin resistance is the likely cause with diets high in saturated fat known to impair insulin sensitivity. Tissue triglyceride composition has been used as marker of dietary intake but it can also be influenced by tissue specific handling of fatty acids. Recent studies have shown that adipocyte insulin sensitivity correlates positively with their saturated fat content, contradicting the common view of dietary effects. A better understanding of factors affecting tissue triglyceride composition is needed to provide further insights into tissue function in lipid metabolism. In this thesis two spectroscopic techniques were developed for in vitro and in vivo analysis of tissue triglyceride composition. In vitro studies (Study I) used infrared spectroscopy (FTIR), a fast and cost effective analytical technique well suited for multivariate analysis. Infrared spectra are characterized by peak overlap leading to poorly resolved absorbances and limited analytical performance. In vivo studies (Studies II, III and IV) used proton magnetic resonance spectroscopy (1H-MRS), an established non-invasive clinical method for measuring metabolites in vivo. 1H-MRS has been limited in its ability to analyze triglyceride composition due to poorly resolved resonances. Using an attenuated total reflection accessory, we were able to obtain pure triglyceride infrared spectra from adipose tissue biopsies. Using multivariate curve resolution (MCR), we were able to resolve the overlapping double bond absorbances of monounsaturated fat and polyunsaturated fat. MCR also resolved the isolated trans double bond and conjugated linoleic acids from an overlapping background absorbance. Using oil phantoms to study the effects of different fatty acid compositions on the echo time behaviour of triglycerides, it was concluded that the use of long echo times improved peak separation with T2 weighting having a negligible impact. It was also discovered that the echo time behaviour of the methyl resonance of omega-3 fats differed from other fats due to characteristic J-coupling. This novel insight could be used to detect omega-3 fats in human adipose tissue in vivo at very long echo times (TE = 470 and 540 ms). A comparison of 1H-MRS of adipose tissue in vivo and GC of adipose tissue biopsies in humans showed that long TE spectra resulted in improved peak fitting and better correlations with GC data. The study also showed that calculation of fatty acid fractions from 1H-MRS data is unreliable and should not be used. Omega-3 fatty acid content derived from long TE in vivo spectra (TE = 540 ms) correlated with total omega-3 fatty acid concentration measured by GC. The long TE protocol used for adipose tissue studies was subsequently extended to the analysis of liver fat composition. Respiratory triggering and long TE resulted in spectra with the olefinic and tissue water resonances resolved. Conversion of the derived unsaturation to double bond content per fatty acid showed that the results were in accordance with previously published gas chromatography data on liver fat composition. In patients with metabolic syndrome, liver fat was found to be more saturated than subcutaneous or visceral adipose tissue. The higher saturation observed in liver fat may be a result of a higher rate of de-novo-lipogenesis in liver than in adipose tissue. This thesis has introduced the first non-invasive method for determining adipose tissue omega-3 fatty acid content in humans in vivo. The methods introduced here have also shown that liver fat is more saturated than adipose tissue fat.

Note on the locally product and almost locally product structures

This paper is concerned with a study of some of the properties of locally product and almost locally product structures on a differentiable manifold X n of class C k . Every locally product space has certain almost locally product structures which transform the local tangent space to X n at an arbitrary point P in a set fashion: this is studied in Theorem (2.2). Theorem (2.3) considers the nature of transformations that exist between two co-ordinate systems at a point whenever an almost locally product structure has the same local representation in each of these co-ordinate systems. A necessary and sufficient condition for X n to be a locally product manifold is obtained in terms of the pseudo-group of co-ordinate transformations on X n and the subpseudo-groups [cf., Theoren (2.1)]. Section 3 is entirely devoted to the study of integrable almost locally product structures.