Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

D-MG Tradeoff and Optimal Codes for a Class of AF and DF Cooperative Communication Protocols

Cooperative relay communication in a fading channel environment under the orthogonal amplify-and-forward (OAF), nonorthogonal and orthogonal selection decode-and-forward (NSDF and OSDF) protocols is considered here. The diversity-multiplexing gain tradeoff (DMT) of the three protocols is determined and DMT-optimal distributed space-time (ST) code constructions are provided. The codes constructed are sphere decodable and in some instances incur minimum possible delay. Included in our results is the perhaps surprising finding that the orthogonal and the nonorthogonal amplify-and-forward (NAF) protocols have identical DMT when the time durations of the broadcast and cooperative phases are optimally chosen to suit the respective protocol. Moreover our code construction for the OAF protocol incurs less delay. Two variants of the NSDF protocol are considered: fixed-NSDF and variable-NSDF protocol. In the variable-NSDF protocol, the fraction of time occupied by the broadcast phase is allowed to vary with multiplexing gain. The variable-NSDF protocol is shown to improve on the DMT of the best previously known static protocol when the number of relays is greater than two. Also included is a DMT optimal code construction for the NAF protocol.

Theoretical studies on the conformation of beta-D-N-acetyl neuraminic acid (sialic acid)

The possible conformations of sialic acid were analysed using semi-empirical potential functions. The solid state conformation has approx. 0.2 kcal/mol higher energy than the minimum energy conformation. These studies suggest that in solution sialic acid may exist preponderantly in two different conformations which differ in the orientation of the terminal hydroxymethyl group of glycerol side-chain. The present model is consistent with 1H- and 13C-NMR data, but differs from the earlier models.

Superconformal transformations of theN = 2,D = 4, SSYM

We obtain the superconformal transformation laws for theN=2,D=4 SSYM. The transformations involve Yang-Mills fields and the corresponding field strength tensor is not constrained to be self antidual. We explicitly demonstrate the closure of the superconformal algebra.

An interactive graphics system for 2-D drawing and design

This paper is about a software system, GRASS-Graphic Software System for 2-D drawing and design—which has been implemented on a PDP-11/35 system with RSX-11M operating system. It is a low cost interactive graphics system for the design of two dimensional drawings and uses a minimum of hardware. It provides comprehensive facilities for creating, editing, storing and retrieving pictures. It has been implemented in the language Pascal and has the potential to be used as a powerful data-imputting tool for a design-automation system. The important features of the system are its low cost, software character generation and a user-trainable character recognizer, which has been included.

The modes of binding methyl-alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A--a theoretical approach

The probable modes of binding of Methyl--alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A have been proposed from theoretical studies. Theory predicts that beta-MeGlcP can bind to ConA in three different modes whereas alpha-MeGlcP can bind only in one mode. beta-MeGlcP in its most favourable mode of binding differs from alpha-MeGlcP in its alignment in the active-site of the lectin where it binds in a flipped or inverted orientation. Methyl substitution at the C-2 atom of the alpha-MeGlcP does not significantly affect the possible orientations of the sugar in the active-site of the lectin. Methyl substitution at C-3 or C-4, however, affects the allowed orientations drastically leading to the poor inhibiting power of Methyl-3-O-methyl-alpha-D-glucopyranoside and the inactivity of Methyl-4-O-methyl-alpha-D-glycopyranoside. These studies suggest that the increased activity of the alpha-MeGlcP over beta-MeGlcP may be due to the possibility of formation of better hydrogen bonds and to hydrophobic interactions rather than to steric factors as suggested by earlier workers. These models explain the available NMR and other binding studies.

Kinetic mechanism of the interaction of D-cycloserine with serine hydroxymethyltransferase

The kinetic mechanism for the interaction of D-cycloserine with serine hydroxymethyltransferase (EC2.1.2.1) from sheep liver was established by measuring changes in the activity, absorbance, and circular dichoism (CD) of the enzyme. The irreversible inhibition of the enzyme was characterized by three detectable steps: an initial rapid step followed by two successive steps with rate constants of 5.4 X s-l and 1.4 X lo4 s-l. The first step was distinguished by a rapid disappearance of the enzyme absorbance peak at 425 nm, a decrease in the enzyme activity to 25% of the uninhibited velocity, and a lowering of the CD intensity at 432 nm to about 65% of the original value. The second step of the interaction was accompanied by a complete loss of enzyme.

Self-assembly of three new coordination complexes: Formation of 2-D square grid, 1-D chain and tape structures

Three distinct coordination complexes, viz., [Co(imi)(2)(tmb)(2)] (1) [where imi = imidazole], {[Ni(tmb)(2)(H2O)(3)]center dot 2H(2)O}(n) (2) and [Cu-2(mu-tmb)(4)(CH3OH)(2)] (3), have been synthesized hydrothermally by the reactions of metal acetates,2,4,6-trimethylbenzoic acid (Htmb) and with or without appropriate amine. The Ni analogue of 1 and the Co analogue of 2 have also been synthesized. X-ray single-crystal diffraction suggests that complex 1 represents discrete mononuclear species and complex 2 represents a 1D chain coordination polymer in which the Ni(H) ions are connected by the bridging water molecules. Complex 3 represents a neutral dinuclear complex. In 1, the central metal ions are associated by the carboxylate moiety and imidazole ligands, whereas the central metal atom is coordinated to the carboxylate moiety and the respective solvent molecules in 2 and 3. In 3, the four 2,4,6-trimethylbenzoate moieties act as a bridge connecting two copper (11) ions and the 0 atoms of methanol coord geometry, with the methanol molecule at the apical position. In all the three structures the central metal atom sits on a crystallographic inversion centre. In all the cases, the coordination entities are further organized via hydrogen bonding interactions to generate multifarious supramolecular networks. Complexes 1, 2 and 3 have also been characterized by spectroscopic (UV/Vis and IR) and thermal analysis (TGA). In addition, the complexes were found to exhibit antimicrobial activity. The magnetic susceptibility measurements, measured from 8 to 300 K, revealed antiferromagnetic interactions between the Co(II) ions in compound 1 and the Ni(II) ions in la, respectively.

The Crystal Structure of Pivaloyl- D- prolyl-L- prolyl- L-alanyl-N- methylamide

Pivaloyl-D-prolyl-L-prolyl-L-analyl-N-methylam~de (I), C1UH32N40c4r,y stallizes in the orthorhombic space group P21212,w ith four molecules in a unit cell of dimensions a = 9.982 (l),b = 10.183 (3), c = 20.746 (2)A . The structure has been refined to R 0.048 for 1 745 observed reflections. All the peptide bonds in the molecule are trans and both the prolyl residues are in the CY-exo-conformation. The molecule assumes a highly folded conformation in which a Type II' DL bend is followed by a Type I LL bend, both stabilised by intramolecular 4 + 1 hydrogen bonds. This conformation, which has been observed for the first time, is of interest in relation to the structure of gramicidin S.

Studies on follicular atresia: role of tropic hormone and steroids in regulating cathepsin-D activity of preantral follicles of the immature rat

The ovary of the immature female rat is comprised of primary and medium-sized preantral follicles. Upon stimulation with FSH or PMSG, the cathepsin-D activity, a representative lysosomal enzyme of granulosa cells, is reduced by 50% (P < 0.01). 17β-Estradiol at the doses tried was unable to mimic this effect. Blockade of steroidogenesis with cyanoketone also had no effect on the cathepsin-D activity of isolated granulosa cells. Dihydrotestosterone (DHT), however, at a dose of 1 mg/rat was able to inhibit PMSG's tropic action. It brought about an increase in cathepsin-D activity and reduction in steroidogenic activity of isolated granulosa cells. The atretogenic activity of DHT could be relieved by supplementation with exogenous FSH. DHT was observed to significantly reduce (P < 0.01) endogenous FSH and LH levels within 12–18 h of its injection suggesting that its atretic effect was due to its action at the pituitary rather than the gonad. In addition to the above the ability of 15 IU of PMSG to reduce cathepsin-D activity of granulosa cells was also significantly reduced (P < 0.01) if endogenous FSH was neutralized by a specific FSH antiserum. The present study suggests that as far as small and medium-sized primary and preantral follicles are concerned, FSH lack is the essential signal for onset of atresia.

1-D hydrogen-bonded organization of hexanuclear {3d-4f-5d} complexes: evidence for slow relaxation of the magnetization for [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2] with Ln = Tb and Dy

Heterometallic {3d-4f-5d} aggregates with formula [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2]·15H2O, (LMe2 stands for N,N-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff-base ligand) with Ln = Gd, Tb, Dy, have been obtained by reacting bimetallic [LMe2Ni(H2O)2Ln(NO3)3] and Cs3{W(CN)8} in H2O. The hexanuclear complexes are organized in 1-D arrays by means of hydrogen bonds established between the solvent molecules coordinated to Ln and the CN ligands of an octacyanometallate moiety. The X-ray structure was solved for the Tb derivative. Magnetic behavior indicates ferromagnetic {W–Ni} and {Ni–Ln} interactions (JNiW = 18.5 cm-1, JNiGd = 1.85 cm-1) as well as ferromagnetic intermolecular interactions mediated by the H-bonds. Dynamic magnetic susceptibility studies reveal slow magnetic relaxation processes for the Tb and Dy derivatives, suggesting SMM type behavior for these compounds.

Conformational analysis of D-pantothenic acid

The conformational analysis of d-pantothenic acid using classical semiempirical methods has been carried out. The pantothenic acid molecule can exist in the neutral form (I) or in the ionised form (II) with a deprotonated negatively charged carboxyl group. The neutral molecule as well as the anion is highly flexible and has an ensemble of several allowed conformations rather than one or two unique conformations. The distribution of allowed conformations indicate that the β-alanine as well as the pantoic acid part of the molecule prefers partially folded conformations. The conformation of the former is greatly affected by the ionisation state of the carboxyl group whereas that of the latter is not. Possibility of intramolecular hydrogen bonding in different allowed conformations has also been explored. A bifurcated hydrogen bond involving a carboxyl (or carboxylate) oxygen atom and a hydroxyl oxygen atom, as acceptors, and the amide nitrogen atom as the donor occurs frequently in both I and II. Amongst the two crystal structures containing pantothenic acid reported so far, the conformation of the molecule in l-lysine d-pantothenate lies in the allowed region and is stabilised by a bifurcated intramolecular hydrogen bond, whereas that in the calcium bromide salt falls in a disallowed region, presumably due to the requirement of tridentate metal coordination.

Sequence effects in structures of the dinucleotides d-pApT AND d-pTpA

The H1',H2' and H2″ regions of the 270-MHz PMR spectra of two deoxydinucleotides, d-pTpA and d-pApT, have been analyzed. The coupling constants in the sugar ring indicate that both A and T sugars have a tendency to acquire 2E conformations. There is also a marginal difference in the 2E populations of the T sugar in the two dinucleotides. The trends in the chemical shifts of base protons indicate different stacking of the bases in d-pApT and d-pTpA. The sequence effects on base stacking and pentose conformation are discussed.