Coiled-coil structure bending

If one traces a longer stretch of a DNA molecule in solution, a clear divergence from linearity becomes evident. Thermally induced structural fluctuations allow a bending of DNA, which is why long DNA molecules are described as a random coil. This bending of the DNA occurs in molecules with a length of more than ca. 200 bp. 

Fig. 1. Secondary structure of E. colt ribosomal proteins LI 1 and SI 1 as predicted from their amino acid sequences. The prediction was carried out using four different methods represented by four different lines (S74, F82, N77, and R76). The line PRE summarizes the secondary structure obtained when at least three out of the four predictions are in agreement. The symbols represent residues in helical (A), turn or bend (B), extended (C), and coil (D) conformational states, respeaively. For details see Wittmann-Liebold et al. (1977b) and Dzionara rl cd. (1977).

Brushes with long side chains can be synthesized by polymerization of macromonomers [117-119] or by grafting of the side chains to [16-20] or from [21] a main chain. In contrast to globular dendrimers, these molecules have an anisotropic primary structure and experience bending or coiling of the molecular contour. Depending on the relative stiffness of the main and side chains, one may distinguish four types of molecular cylinders (Fig. 20). 

That DNA would bend on itself and become super-coiled in tightly packaged cellular DNA would seem logical, then, and perhaps even trivial, were it not for one additional fact many circular DNA molecules remain highly supercoiled even after they are extracted and purified, freed from protein and other cellular components. This indicates that supercoiling is an intrinsic property of DNA tertiary structure. It occurs in all cellular DNAs and is highly regulated by each cell. 

Correct answer = C. p-Bends often contain pro line, which provides a kink. The a-helix differs from the p-sheet in that it always involves the coiling of a single polypeptide chain. The P-sheet occurs in both parallel and antiparallel forms. Motifs are elements of tertiary structure. The a-helix is stabilized primarily by hydrogen bonds between the -C=0 and -NH- groups of peptide bonds. 

The secondary structure of a protein is generally defined as regular arrangements of amino acids that are located near to each other in the linear sequence. Examples of such elements are the a-helix, p-sheet, and P-bend. Some secondary structure is not regular, but rather is considered non-repetitive (loop and coil). 

The structure of proteins determines their function and can be described on four levels, illustrated on page 447. The primary structure is the sequence of amino acids in the polypeptide chain. The secondary structure describes how various short portions of a chain are either wrapped into a coil called an alpha helix or folded into a thin pleated sheet. The tertiary structure is the way in which an entire polypeptide chain may either twist into a long fiber or bend into a globular clump. The quaternary structure describes how separate proteins may join to form one larger complex. Each level of structure is determined by the level before it, which means that ultimately it is the sequence of amino acids that creates the overall protein shape. Fhis final shape is maintained both by chemical bonds and by weaker molecular attractions between amino acid side groups. 

The regular secondary structures, a helices and /i sheets, are connected by coil or loop regions of various lengths and irregular shapes. A variant of the loop is the f> turn or reverse turn, where the polypeptide chain makes a sharp, hairpin bend, producing an antiparallel / turn in the process. 

In its compact crystal structure, the two opioid tetrapeptide pharmacophores of biphalin are not conformationally equivalent. One tetrapeptide, which has a steric similarity with the delta-selective peptide DADLE, folds into a random coil. The contralateral tetrapeptide, sterically similar to the mu-selective peptide D-TIPP-NH2, exhibits a fairly normal type III (3 bend [4]- These conformational features suggest that under physiological conditions, biphalin may easily bind to these respective opioid receptors. This duality of binding affinity is probably the reason that biphalin is able to interact with all opioid receptor types. 

Polymers assume a rodlike conformation, as opposed to the typical random coil conformation, when the chemical structure (e.g., para connected benzene rings) or molecular folding (e.g., a-helical structures) prevents internal rotation and thus local bending. Examples of such rodlike molecules in biological... 

Most nonfibrous proteins have a very precise and compact three-dimensional or tertiary structure formed when the a-helix and random coil of the polypeptide chain bends, twists, and folds over and back upon itself. The tertiary structure is stabilized by interactions of amino acid R-groups (Fig. 2-4a), and thus, is dictated by the primary structure. The biochemical function of a protein is intimately tied to its tertiary structure. That is, to function in a certain way, a protein must have the correct tertiary structure. Stated conversely only one specific tertiary structure will permit a protein to serve optimally a specific function (see also Figs. 4-3 and 4-4). 

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