Loop structures

CS Ring, FE Cohen. Conformational sampling of loop structures using genetic algorithm. Isr I Chem 34 245-252, 1994. 

Figure S.28 Schematic diagrams of the two-sheet P helix. Three complete coils of the helix are shown in (a). The two parallel P sheets ate colored gieen and red, the loop regions that connect the P strands ate yellow, (b) Each stmctuial unit Is composed of 18 residues forming a P-loop-P-loop structure. Each loop region contains six residues of sequence Gly-Gly-X-Gly-X-Asp where X is any residue. Calcium Ions are bound to both loop regions. (Adapted from F. Jumak et al., Ciirr. Opin. Struct. Biol. 4 802-806, 1994.)...

The detailed analysis of the way in which the overall and internal structure of PCNTs apparently arise is discussed elsewhere[20j. Here, we draw attention to some particularly interesting and unusual structures which occur in the body of the nanotubes. An expansion of the section of the central core which lies ca. 5 below the tip of the nanotube in Fig. 1 is shown in Fig. 2. Loop structures occur at points a-d and a -d in the walls in directly opposing pairs. This parallel behaviour must, on the basis of statistical arguments, be related and we interpret the patterns as evidence for a hemi-toroidal connection between the inner and outer adjacent concentric graphene tubes (i.e., turnovers similar to a rolled-over sock). That the loops, seen in the HRTEM, are evidence for very narrow single-walled closed-ended tubes trapped within the walls can be discounted, also on statistical grounds. 

RNA decoys from HCV stem-loop structures in NS5B coding region sequester replication complexes HCV (Zhang et al. 2005)... 

The bacterial Rieske proteins contain 3—20 extra residues in the catalytic domain these insertions occur in the helix—loop structure and in the loop /35-/S6 (see Section III,B). The insertion of a single residue is observed in some bacterial sequences between the flexible linker and f3 strand 1 as well as in the Pro loop. Twenty-eight residues are fully conserved between 11 mitochondrial and 6 bacterial sequences 22 of these conserved residues are located in the cluster binding subdomain. 

Alternatively, one interesting drug delivery technique exploits the active transport of certain naturally-occurring and relatively small biomacromolecules across the cellular membrane. For instance, the nuclear transcription activator protein (Tat) from HIV type 1 (HlV-1) is a 101-amino acid protein that must interact with a 59-base RNA stem-loop structure, called the traus-activation region (Tar) at the 5 end of all nascent HlV-1 mRNA molecules, in order for the vims to replicate. HIV-Tat is actively transported across the cell membrane, and localizes to the nucleus [28]. It has been found that the arginine-rich Tar-binding region of the Tat protein, residues 49-57 (Tat+9 57), is primarily responsible for this translocation activity [29]. 

Figure 39-19. Structure of a typical eukaryotic mRNA showing elements that are involved in regulating mRNA stability. The typical eukaryotic mRNA has a 5 noncoding sequence (5 NCS), a coding region, and a 3 NCS. All are capped at the 5 end, and most have a polyadenylate sequence at the 3 end. The 5 cap and 3 poly(A) tail protect the mRNA against exonuclease attack. Stem-loop structures in the 5 and 3 NCS, features in the coding sequence, and the AU-rich region in the 3 NCS are thought to play roles in mRNA stability.

Arg-13 in RpII are part of the looped structures. Other work by Kem and... 

The lattice of implications among (1) - (8) and strong equivalence appears below. No implications shown can be reversed and no implications not in the diagram hold. Conditions (7) and (8) represent an attempt to formalize the idea of preserving loop structure, since cycles in P correspond to cycles in P and cycles in P, if repeated often enough, correspond to cycles in P. ... 

The transformation is global. The schemes P and P are strongly computationally equivalent in the restricted sense - if we omit from the test added computational histories of (P,I, a) and (P, I, a) all values of the new variables and all tests involving these variables (i.e. test Z ) for an interpretation I extending I to all of P and P, then the resulting lists are equal. However the loop structure of P has been drastically changed and there is no simple relationship between the graphs of P and P. ... 

The efficiency of translation driven by IRES elements is often significandy lower than that of canonical translation (e.g., Fig. 6.1C) and, thus, control experiments may be needed to demonstrate that genuine IRES activity is measured. This can be done by inserting a stable stem-loop structure into the mRNA 5 UTR, upstream of the IRES element, or by comparing the translational output of a reporter mRNAs with the wild-type IRES to that of the equivalent transcript harboring a mutated, inactive IRES element (which should be much lower Humphreys et al, 2005 Wilson et al, 2000). 

While RNA molecules do not have the double stranded structure usually found in DNA, in many RNA molecules stem-loop structures are found in which the anti-parallel strands are connected by a 5-7 residue loop. Rather like the P-tum in proteins, this allows the... 

Figure 1. Hierarchical model of chromosome structure, (a) In interphase cells, DNA is packed in a nucleus as forming nucleosome and chromatin, (b) DNA forms nucleosome structure together with core histone octamer, which is then folded up into 30nm fiber with a help of linker histone HI. This 30 nm fiber is further folded into 80 nm fiber and 300 nm loop structures in a nucleus. In mitosis, chromosome is highly condensed. Proteins which are involved in each folding step are indicated above and non-protein factors are indicated below, (c) The amino acid sequences of histone tails (H2A, H2B, H3 and H4) are shown to indicate acetylation, methylation and phosphorylation sites. (See Colour Plate 1.)...

Palmer DK, O Day K, Margolis RL (1990) The centromere specific histone CENP-A is selectively retained in discrete foci in mattunaUan sperm nuclei. Chromosoma 100 32—36 Pandey NB, Marzluff WF (1987) The stem-loop structure at the 3 end of histone mRNA is necessary and sufficient for regulation of histone mRNA stabiUty. Mol Cell Biol 7 4557 559 Pehrson J, Fuji RN (1998) Evolutionary conservation of histone macroH2A subtypes and domains. Nucl Acids Res 26 2837-2842... 

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