Hairpin turns

The specific nature of the reentry loops is not the point of this illustration. The sketch shows both hairpin turns and longer loops. Problem 7 at the end of the chapter examines the actual nature of the reentry loop. 

The availability of sequence-specific DNA binding molecules led to the development of bifunctional polyamides that covalently react with the minor groove of DNA. Two classes of alkylating agents were conjugated to the hairpin turn unit and bound proximal to their alkylation sites by a DNA-binding polyamide [58, 59]. 

FIGURE 2.15 Structure of a spherulite from the bulk, (b) A slice of a simple spherulite. As further growth occurs, filling in, branch points, etc. occur as shown in (a). The contour lines are simply the hairpin turning points for the folded chains. 

One strategy to control folding is to direct folds by introduction of S-hairpins, turns which are often associated with Pro incorporation in a polypeptide sequence. Constrained turn mimics have previously been employed in investigations of the active conformation of peptides. Clearly, from the above discussion of CyP and... 

Rho-independent termination of transcription. A. An example of a palindrome in double-stranded DNA. B. A transcribed DNA palindrome codes for RNA that can form a hairpin turn. 

Besides hairpin turns and broader U-tums, a protein chain may turn out and fold back to reenter a P sheet from the opposite side. Such crossover connections, which are necessarily quite long, often contain helices. Like turns, crossover connections have a handedness and are nearly always right-handed (Fig. 2-25).117/219 Most proteins also contain poorly organized loops on their surfaces. Despite their random appearance, these loops may be critical for the functioning of a protein.220 In spite of the complexity of the folding patterns, peptide chains are rarely found to be knotted.221... 

The DNA double helix is not necessarily the continuous smooth structure shown in Figure 10.20. There may be bulges of various sorts, loops, and palindromic hairpin turns. A palindrome is a section of DNA in which the two DNA strands have an identical base sequence running in opposite directions. Figure 10.23 shows a double-stranded DNA with some such features. Of most interest are the cruciform bulges and palindromic structures. Note that in the cruciform structure, there are two pairs of palindromic sequences on the vertical... 

Transfer RNA (tRNA) has the lowest molecular weight, that is, near 28,000. Its function is to activate amino acids for protein biosynthesis. It has a unique cloverleaf structure (Figure 10.29), and there are sections of double-helix, bulges, and hairpin turns. Of all RNAs, it has the highest number of unusual bases (10-15%). Thus, the hairpin arm pointing east contains pseudouridine W and is... 

Fig. 13. (a) /(-Turn conformation of the Cys-X-Y-Cys fragment coordinating to the Fe4S42+ core and (b) /(-II hairpin turn conformation of a tetrapeptide fragment. 

Fio. 19. Schematic structure of the 20-peptide/Fe2S22 + complex speculated by the energy minimum calculations (65). Large open circles represent a-carbon atoms. Closed circles show Fe(III) and sulfur atoms. Small open circles refer to carbon and nitrogen atoms involved in the artificial hairpin turn and Cys CH2 carbons. One NH—OC hydrogen bond (dashed line) is expected at the hairpin turn. 

Shape and dimension, (a) Tropomyosin, a 70-kd muscle protein, is a two-stranded a-helical coiled coil. Estimate the length of the molecule, (h) Suppose that a 40-residue segment of a protein folds into a two-stranded antiparallel P structure with a 4-residue hairpin turn. What is the longest dimension of this motif ... 

We can ask whether a particular sequence by itself folds into an a helix, p strand, or hairpin turn or behaves as a random coil. 

Fig. 9 Multiblock copolymers consisting of a poly(ethylene glycol) soft block and a tetrapeptide Ala-Gly-Ala-Gly, crystalline hard block in two variants a Templated system in which an aromatic hairpin turn is used to force parallel jS-sheet formation, b Non-templated system in which peptide segments are free to form parallel and/or antiparallel /1-sheets. Reprinted with permission from [43]. Copyright 2001 American Chemical Society...

Two forms of j8-tums. Each is a tetrapeptide and accomplishes a hairpin turn. The amino acid residues are identified by numbering the a-carbons 1. The CO group of residue 1 is hydrogen-bonded to the NH group of residue 4. Structure (b) is stable only if a glycine (R = H) residue is present as the third residue because of steric hindrance between the R-group and the carbonyl oxygen (double-headed arrow). 

The construction of "a calixarene with four peptide loops" serves two functions in this article. It serves as a simplified substitute for an antibody, though we doubt that the intent of the authors is the design of potential therapeutic agents. More important, the calixarene serves to test the theory of antibody function sketched in the preceding discussion Is this really the way that antibodies work The authors note that earlier attempts to mimic antibodies have been unsuccessful, and they propose the alternative strategy, which is the heart of the article The search for antibody mimics has not yet yielded compact and robust frameworks that reproduce the essential features of the CDRs. Our strategy is to use a macrocyclic scaffold to which multiple peptide loops in stable hairpin-turn conformations can be attached (p. 2681). 

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