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Conformational Changes in Nucleic Acids Modified by Chemical Carcinogens
Published in Philip L. Grover, Chemical Carcinogens and DNA, 2019
D. Grunberger, I. B. Weinstein
Possible explanations for the above results were sought with CPK space-filling models. A plausible model for G*pU II or G*pU IV, the two 9,10 trans products, is shown schematically in Figure 17. Starting with a dimer having the usual conformational parameters of RNA (see Section I), an alteration in conformation which maximizes stacking interaction between the pyrene ring system and the neighboring uracil was achieved, largely by rotating the guanine residue about 45° around its glycosidic bond. In this conformation, the plane of the pyrene ring is perpendicular to the long axis of the phosphate-sugar backbone, and the displaced guanine is no longer coplanar to the neighboring uracil. At the same time, the hydrophilic hydroxyls of the BPDE residue face the ribose of the modified G.
Fungal Sterols
Published in Rajendra Prasad, Mahmoud A. Ghannoum, Lipids of Pathogenic Fungi, 2017
Fungal sterols consist of the cyclopentanoperhydrophenanthrene tetracyclic nucleus with an equatorial 3β-hydroxy group, α-methyl groups at C-10 and C-13 and an eight to ten carbon side chain at C-17. The principal fungal sterol is ergosterol. It was first isolated in 1889,1 and has been shown to be produced by 558 fungal cultures covering 60 species in 20 genera.2 Ergosterol differs from cholesterol, the principal animal sterol, in that the fungal sterol has double bonds at C-7 and C-22 and a methyl substituent at C-24 with the configuration, 24R. Ergosterol is thus named 24-methyl-cholesta-5,7,22-(trans)-trien-3β-ol. The ergosterol structure with numbering and space-filling models is shown in Figure 1. In the limited space that is available for this review, it is impossible to detail the myriad of sterols found in fungi or to discuss the individual fungal species. Excellent treatments of these subjects have been reported and should be consulted for definitive work on sterol synthesis and taxonomic distribution.3,4
Cross-Linking of Collagen
Published in Marcel E. Nimni, Collagen, 1988
Mitsuo Yamauchi, Gerald L. Mechanic
A controversy has existed concerning the number of molecules in a fibril linked by PYR. Some investigators have suggested that it links three molecules,23 while others favor a linkage between two molecules.4 The latter seems to be favored because the formation of the crosslink would require only nearest-neighbor molecules; therefore less constraints are imposed on the organization of molecules in the fibril. A linkage among three molecules by the crosslink would require four molecules to be correctly staggered and juxtaposed in the fibril for its formation, which is unlikely. The measurement of the bond distances between the backbone α-carbon atoms of the PYR, in a CPK space-filling model (0.49 nm and 1.07 nm),54 collagen model building, and molecular calculation63 also suggest the formation of PYR involving only two molecules. In support of this, it has recently been shown that the peptidyl residues of Lys and Hyl in the COOH-terminal nonhelical regions of both al (I) chains, in a molecule of type I collagen, are quantitatively converted to aldehyde. These, in turn, stoichiometrically condense with the ε-amino groups of helical residues of Hyl-87 on all three chains of the nearest neighboring collagen molecule in periodontal ligament.1 These positions, when they come together to form the cross-link, become the major locus of PYR.2,55,94
Thermo-sensitive self-assembly of poly(ethylene imine)/(phenylthio) acetic acid ion pair in surfactant solutions
Published in Drug Delivery, 2022
The self-assembly of amphiphilic molecules is spontaneously formed in an aqueous solution via an entropy-driven process (Tanford, 1973; Israelachvili et al., 1980; Michel & Cleaver, 2007; Sorrenti et al., 2013). A major determinant for the shape and the structure of the self-assembly is the shape of amphiphilic molecules because amphiphilic molecules act as the building block and constitute the assembly following a space-filling model. The shape of amphiphilic molecules can be characterized by the packing parameter (P) (Tanford, 1973; Khalil & Zarari, 2014; Lombardo et al., 2015; Doncom et al., 2017; Lombardo et al., 2020). If the packing parameter is around 1, an amphiphilic molecule is rectangular and it can build up bilayer. If the packing parameter is much different from 1, an amphiphilic molecule is conical (P < 1) or reversed conical (P > 1) and it can be assembled into micelles or hexagonal phase (Tanford, 1973; Sych et al., 2018; Sagnella et al., 2010; N. Wang et al., 2019). Much attention has been paid to self-assembly for its use as a drug carrier because it shows the versatile property in several aspects.
Update of the GRIP web service
Published in Journal of Receptors and Signal Transduction, 2020
Akira Saito, Daiki Tsuchiya, Seiji Sato, Atsushi Okamoto, Yoichi Murakami, Kenji Mizuguchi, Hiroyuki Toh, Wataru Nemoto
As an example, the result of the interface prediction for human D1 dopamine receptor (hD1R) is shown on the structure of the D3 dopamine receptor (3PBL chain A) in Figure 4. The predicted interface residues of hD1R are provided in the table on the right side of the page. Each predicted interface residue is indicated by a space-filling model on the graphics of the structure, by clicking the button on the left side of the residue number in the table. The first predicted interface residues exist on Gly, Leu, and Pro on TM helix VI, and Trp on helix VII. The second predicted interface is close to the first predicted interface in space.