Antiparallel strands

Assume that we have eight antiparallel p strands arranged in a barrel structure. We decide that we want to connect strand number n to an antiparallel strand at the same end of the barrel. We do not want to connect it to strand number n -e 1 as in the up-and-down barrels just described, nor do we want to connect it to strand number n - 1 which is equivalent to turning the up-and-down barrel in Figure 5.2 upside down. What alternatives remain ... 

The major stmctural feature of the HAz chain (blue in Figure 5.20) is a hairpin loop of two a helices packed together. The second a helix is 50 amino acids long and reaches back 76 A toward the membrane. At the bottom of the stem there is a i sheet of five antiparallel strands. The central i strand is from HAi, and this is flanked on both sides by hairpin loops from HAz. About 20 residues at the amino terminal end of HAz are associated with the activity by which the vims penetrates the host cell membrane to initiate infection. This region, which is quite hydrophobic, is called the fusion peptide. 

Two antiparallel helices, related by space group symmetry, are packed in an orthorhombic unit cell (Fig. 39b). There is substantial interdigitation between the helices so that side chains and main chains are linked by hydrogen bonds, such as 0-4E-0-4D (2,73 A) and 0-4D-0-3F (2.84 A) involving parallel and antiparallel strands, respectively. Plausible sites for sodium ions are near the... 

The antiparallel strand structure between residues 131 and 238 in the cytoplasmic portion of Ca -ATPase was originally designated as transduction domain the name suggested its possible role in the conformational coupling between the nucleotide binding and phosphorylation sites exposed to the cytoplasm and the Ca channel located at some distance from each other in the lipid bilayer [8,42]. The site specific mutagenesis of conserved amino acids in the P strand sector of the molecule provides support for its proposed function in conformational transitions [103,126,127,215]. 

A sequence, in general, is the relative order of base pairs, whether in a fragment of a protein, DNA, a gene, a chromosome, or an entire genome. DNA is composed of two antiparallel strands of deoxynucleotides held together by hydrogen bonds between purine (adenine, A and guanine, G) and pyrimidine (thymidine, T uracil, U and cytosine, C) bases. 

A = Adenine = purine T = Thymine = pyrimidine G = Guanine = purine C = Cytosine = pyrimidine U = Uracil = pyrimidine AT/GC base pairs Antiparallel strands Major groove-minor groove A-, B-, and Z-DNA... 

Ambrus, A., Chen, D., Dai, J., Biabs, T., Jones, R.A. and Yang, D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution, Nucleic Acids Res., 34, 2723-2735. 

AT/GC base pairs Antiparallel strands Major groove-minor groove A-, B-, and Z-DNA... 

CNS drugs antiparallel strands inside the folded structure are mainly found four of the disulfide-bonded cysteine residues Kohno 1995, and its synthetic version SNX-111... 

The X-ray diffraction patterns obtained from potassium hyaluronate films prepared from solutions of pH 3.0-4.0 were representative of the patterns from Rb+, Cs+, and NH4 forms. At 90-98% r.h., the unit cell is tetragonal, with a = b = 1.714 nm, and c = 3.28 nm. Each chain is a 4(— 0.82) helix, and two such chains fonn an antiparallel-stranded double-helix. There are two double helices in the unit cell, and the space group is 14,22. There are no intramolecular hydrogen-bonds. 

DNA in cells exists mainly as double-stranded helices. The two strands in each helix wind about each other with the strands oriented in opposite directions (antiparallel strands). The bases of the nucleotides are directed toward the interior of the helix, with the negatively charged phosphodiester backbone of each strand on the outside of the helix. This is the famous B-DNA double helix discovered by Watson and Crick (Figure 3.3). 

The conformation of BESOD has been determined by X-ray diffraction to a resolution of 0.3 nm and of 0.2 nm, as quoted in Almost 50% of the amino-acid residues form a p barrel made up of 8 antiparallel strands. There is a... 

The complementary antiparallel strands of DNA follow the pairing rules proposed by Watson and Crick. The base-paired antiparallel strands differ in base composition the left strand has the composition A3 T2 G, the right, A2 T3 G3 C,. They also differ in sequence when each chain is read in the 5 — 3 direction. Note the base equivalences A = T and G = C in the duplex. 

Figure 9. The relationship between a half-turn and a node. A trefoil knot has been drawn with thick lines its polarity is shown by the arrowheads along the knot. A dashed box has been drawn about each node, so that the strands of the knot divide the boxes into four regions, two between antiparallel strands, two between parallel strands. A half-turn of base pairs is drawn between antiparallel strands the helix axes are shown as double-headed arrows and dyad axes normal to them are represented by dotted lines ending in two ellipses.

Figure 11. Antijunctions and mesojunctions. (a) A 949 knot drawn in a DNA context. Each of the nodes of this knot is shown to be formed from a half-turn of double helical DNA. The polarity of the knot is indicated by the arrowheads passing along it. Various enclosed areas contain symbols indicating the condensation of nodes to form figures. The curved double-headed arrow indicates the condensation of two half-turns into a full turn, the solid triangle indicates a three-arm branched junction, the empty square indicates a 4-strand antijunction, and the shaded square is a four-strand mesojunction. (b) Schematic drawings of 3-strand and 4-strand junctions, antijunctions, and mesojunctions shown as the helical arrangements that can flank a triangle or a square. Each polygon is formed from strands of DNA that extend beyond the vertices in each direction. The arrowheads indicate the 3 ends of the strands. The vertices correspond to the nodes formed by a half-turn of double helical DNA. Base pairs are represented by lines between antiparallel strands. Thin double-headed arrows perpendicular to the base pairs represent the axis of each helical half-turn. The lines perpendicular to the helix axes terminating in ellipses represent the central dyad axes of the helical half-turns. The complexes 33 and 44 correspond to conventional branched junctions. The complex 40 is a 4-strand antijunction. The complexes on the bottom row are mesojunctions, which contain a mix of the two orientations of helix axes.

A biochemical curiosity is the presence in egg white of the glycoprotein avidin.ab Each 68-kDa subunit of this tetrameric protein binds one molecule of biotin tenaciously with Kf 1015 M 1. Nature s purpose in placing this unusual protein in egg white is uncertain. Perhaps it is a storage form of biotin, but it is more likely an antibiotic that depletes the environment of biotin. A closely similar protein streptavidin is secreted into the culture medium by Streptomyces avidinii.c Its sequence is homologous to that of avidin. It has a similar binding constant for biotin and the two proteins have similar three-dimensional structures.3/d i Biotin binds at one end of a P barrel formed from antiparallel strands and is held by multiple hydrogen bonds and a conformational alteration that allows a peptide loop to close over the bound vitamin. 

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