Short Loop Length Research Articles

Molecular Dynamics Simulations to Determine the Optimal Loop Length in the Helix-loop-helix Motif

In this study, 100 ps molecular dynamics simulations were conducted to determine the optimal length of the Gly loop in the helix-loop-helix motif. The results revealed that the length of the loop significantly affected the stability of the two a-helices. In addition, the optimal loop length to maintain the highest helicity of the target peptide was found to be the one corresponding to 7 Gly residues. Longer loop length resulted in structural destabilization due to the entropic effect, while shorter loop length was not suitable to achieve intrachain packing of the two α-helices.

Mechanism of Tet repressor induction by tetracyclines: length compensates for sequence in the α8-α9 loop

Natural Tet repressor (TetR) variants are α-helical proteins bearing a large loop between helices 8 and 9, which is variable in sequence and length. We have deleted this loop consisting of 14 amino acid residues in TetR(D) and rebuilt it stepwise with up to 42 alanine residues. All except the mutant with the longest alanine loop show wild-type repression, but none is inducible with tetracycline. This demonstrates the importance of the α8-α9 loop and its amino acid sequence for induction. The induction efficiencies increase with loop length, when the more tightly binding inducer anhydrotetracycline is used. The largest increase of inducibility was observed for TetR mutants with loop lengths between eight and 17 alanine residues. Since loop residues Asp/Glu157 and Arg158 are conserved in the natural TetR sequence variants, we constructed a mutant in which all other residues of the loop were replaced by alanine. This mutant exhibits increased anhydrotetracycline induction compared to the corresponding alanine variant. Thus, these residues are important for induction. Binding constants for the anhydrotetracycline-TetR interaction are below the detection level of 105 M−1 for the mutant with a loop of two alanine residues and increase sharply until a loop size of ten residues is reached. TetR variants with longer loops have similar anhydrotetracycline-binding constants, ranging between 2.6×109 M−1 and 8.0×109 M−1, about 500-fold lower than wild-type TetR. The increase of the affinity occurs at shorter loop lengths than that of inducibility. We conclude that the induction defect of the polyalanine variants arises from two increments: (i) the loop must have a minimal length to allow efficient inducer binding; (ii) the loop must structurally participate in the conformational change associated with induction.

Steady and nonsteady siphon flow in hot coronal loops

Siphon flow in hot coronal loops is examined, in both its steady and dynamic states, in the latter case using a flux-corrected transport simulation. We find that such flows are inhibited by (1) low heating rates, (2) high pressures, (3) short loop lengths, and (4) turbulence. In accordance with expectations, we find that small footpoint pressure asymmetries produce steady subsonic flow. However, the standard picture that larger values yield standing shocks is shown to be valid only for sufficiently high heating, long loops, or low pressure. Values of these parameters more characteristic of active regions produce instead a quasi-periodic surge flow when the pressure asymmetry exceeds a critical value at which the temperature gradient at the inflow end reverses sign. These flows are normally subsonic, though examples can be found where the surge is supersonic for a part of each period. The difficulty of driving substantial siphon flows for realistic hot loop models is in accordance with the comparative rarity of observations of these flows. 37 refs.