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Der Waals Contact (der + waal_contact)
Selected AbstractsDynamic Molecular Tweezers Composed of Dibenzocyclooctatetraene Units: Synthesis, Properties, and Thermochromism in Host,Guest ComplexesCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2009Tomohiko Nishiuchi Abstract Novel dynamic molecular tweezers (DMTs) 3,a, 3,b, 4,a, 4,b, and 5,b, composed of two tub-shaped dibenzocyclooctatetraene (DBCOT) units, were designed and synthesized. The cyclooctatetraene (COT) rings of these DMTs readily invert in solution, and the molecular structure shows rigid syn and anti forms in an equilibrium mixture in solution. The syn and anti conformers can be observed by NMR. The isomerization barriers of 3,a, 3,b, 4,a, 4,b, and 5,b are in the range of 16.5,21.3,kcal,mol,1, depending on steric repulsion between substituents of the COT rings and protons of the central benzene ring. These DMTs form complexes with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and 1,2,4,5-tetracyano-benzene (TCNB) in solution and in the solid state. The binding abilities of these DMTs increase with electron-donating substituents on COT, which increase the electron densities of the cavity of the syn form, as supported by theoretical calculations. In addition, elongation of the terminal alkoxy chains of the DMTs was found to cause the enhancement of van,der Waals contact with guest molecules. Therefore, 5,b, which has CH2OMe groups on the COT rings and longer ethoxy groups on the terminal benzene rings, showed the highest electron density of the cavity and hence the highest binding ability with the electron-deficient guest molecules. Interestingly, solutions of 3,b, 4,b, and 5,b show thermochromism in the presence of DDQ. A solution of 3,b or 4,b with DDQ in CHCl3 is green due to charge-transfer interaction at room temperature and the color changes from green to yellow upon heating to 60,°C and from green to blue upon cooling to ,40,°C, whereas the high complexation ability of 5,b with DDQ only shows a change in the shade of blue. [source] Solution Structure of a DNA Duplex Containing a Biphenyl PairCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2008Zeena Johar Abstract Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability. Here we present an NMR structure of the decamer duplex d(GTGACXGCAG), d(CTGCYGTCAC) that contains one such X/Y biaryl pair. X represents a 3,,,5,,-dinitrobiphenyl- and Y a 3,,,4,,-dimethoxybiphenyl C -nucleoside unit. The experimentally determined solution structure shows a B-DNA duplex with a slight kink at the site of modification. The biphenyl groups are intercalated side by side as a pair between the natural base pairs and are stacked head to tail in van der Waals contact with each other. The first phenyl rings of the biphenyl units each show tight intrastrand stacking to their natural base neighbors on the 3,-side, thus strongly favoring one of two possible interstrand intercalation structures. In order to accommodate the biphenyl units in the duplex the helical pitch is widened while the helical twist at the site of modification is reduced. Interestingly, the biphenyl rings are not static in the duplex but are in dynamic motion even at 294,K. [source] Effect of sequence polymorphism and drug resistance on two HIV-1 Gag processing sitesFEBS JOURNAL, Issue 16 2002Anita Fehér The HIV-1 proteinase (PR) has proved to be a good target for antiretroviral therapy of AIDS, and various PR inhibitors are now in clinical use. However, there is a rapid selection of viral variants bearing mutations in the proteinase that are resistant to clinical inhibitors. Drug resistance also involves mutations of the nucleocapsid/p1 and p1/p6 cleavage sites of Gag, both in vitro and in vivo. Cleavages at these sites have been shown to be rate limiting steps for polyprotein processing and viral maturation. Furthermore, these sites show significant sequence polymorphism, which also may have an impact on virion infectivity. We have studied the hydrolysis of oligopeptides representing these cleavage sites with representative mutations found as natural variations or that arise as resistant mutations. Wild-type and five drug resistant PRs with mutations within or outside the substrate binding site were tested. While the natural variations showed either increased or decreased susceptibility of peptides toward the proteinases, the resistant mutations always had a beneficial effect on catalytic efficiency. Comparison of the specificity changes obtained for the various substrates suggested that the maximization of the van der Waals contacts between substrate and PR is the major determinant of specificity: the same effect is crucial for inhibitor potency. The natural nucleocapsid/p1 and p1/p6 sites do not appear to be optimized for rapid hydrolysis. Hence, mutation of these rate limiting cleavage sites can partly compensate for the reduced catalytic activity of drug resistant mutant HIV-1 proteinases. [source] The structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emissionACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Tatsuki Ebisawa Monomeric Azami-Green (mAG) from the stony coral Galaxea fascicularis is the first known monomeric green-emitting fluorescent protein that is not a variant of Aequorea victoria green fluorescent protein (avGFP). These two green fluorescent proteins are only 27% identical in their amino-acid sequences. mAG is more similar in its amino-acid sequence to four fluorescent proteins: Dendra2 (a green-to-red irreversibly photoconverting fluorescent protein), Dronpa (a bright-and-dark reversibly photoswitchable fluorescent protein), KikG (a tetrameric green-emitting fluorescent protein) and Kaede (another green-to-red irreversibly photoconverting fluorescent protein). To reveal the structural basis of stable green emission by mAG, the 2.2,Å crystal structure of mAG has been determined and compared with the crystal structures of avGFP, Dronpa, Dendra2, Kaede and KikG. The structural comparison revealed that the chromophore formed by Gln62-Tyr63-Gly64 (QYG) and the fixing of the conformation of the imidazole ring of His193 by hydrogen bonds and van der Waals contacts involving His193, Arg66 and Thr69 are likely to be required for the stable green emission of mAG. The crystal structure of mAG will contribute to the design and development of new monomeric fluorescent proteins with faster maturation, brighter fluorescence, improved photostability, new colours and other preferable properties as alternatives to avGFP and its variants. [source] | ||||||||||